Starting phenix.real_space_refine on Mon Jun 30 00:07:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgo_44519/06_2025/9bgo_44519.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgo_44519/06_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_44519/06_2025/9bgo_44519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgo_44519/06_2025/9bgo_44519.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgo_44519/06_2025/9bgo_44519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgo_44519/06_2025/9bgo_44519.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 89 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 10.77, per 1000 atoms: 0.31 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: 8.91 Conformation dependent library (CDL) restraints added in 4.6 seconds 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: 3.02 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: 12.19 Time building geometry restraints manager: 10.49 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: 0.31 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 11.710 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: 1.310 Check model and map are aligned: 0.250 Set scattering table: 0.280 Process input model: 64.990 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.13), 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 TRP 0.000 0.000 TRP A 397 HIS 0.001 0.000 HIS G 198 PHE 0.006 0.001 PHE E 411 TYR 0.005 0.001 TYR F 363 ARG 0.003 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.11109 ( 2880) hydrogen bonds : angle 4.68703 ( 8532) covalent geometry : bond 0.00237 (35268) covalent geometry : angle 0.60332 (47556) *********************** 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 : 3.719 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: 0.4711 time to fit residues: 288.2297 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 : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 20.0000 chunk 354 optimal weight: 50.0000 chunk 196 optimal weight: 30.0000 chunk 121 optimal weight: 9.9990 chunk 239 optimal weight: 30.0000 chunk 189 optimal weight: 20.0000 chunk 366 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 223 optimal weight: 50.0000 chunk 273 optimal weight: 220.0000 chunk 424 optimal weight: 8.9990 overall best weight: 9.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 GLN C 277 GLN C 405 ASN E 405 ASN F 405 ASN H 405 ASN I 405 ASN J 405 ASN K 277 GLN L 405 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.063183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.053078 restraints weight = 377903.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.053818 restraints weight = 290945.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.054321 restraints weight = 240187.704| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35268 Z= 0.141 Angle : 0.564 8.767 47556 Z= 0.308 Chirality : 0.038 0.133 5460 Planarity : 0.004 0.044 6552 Dihedral : 3.458 16.621 5064 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.17 % Allowed : 6.47 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.13), residues: 4668 helix: 2.80 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.91 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 397 HIS 0.004 0.001 HIS C 198 PHE 0.017 0.002 PHE A 443 TYR 0.009 0.001 TYR B 240 ARG 0.004 0.000 ARG K 357 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 2880) hydrogen bonds : angle 3.80576 ( 8532) covalent geometry : bond 0.00291 (35268) covalent geometry : angle 0.56397 (47556) *********************** 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 329 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 323 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.1165 (mmp) cc_final: 0.0675 (mmm) REVERT: A 267 MET cc_start: 0.8964 (tpp) cc_final: 0.8204 (ttt) REVERT: B 237 PHE cc_start: 0.8630 (t80) cc_final: 0.8278 (t80) REVERT: B 324 MET cc_start: 0.8342 (mmp) cc_final: 0.8011 (mmm) REVERT: B 405 ASN cc_start: 0.8821 (m-40) cc_final: 0.8579 (m110) REVERT: B 429 LYS cc_start: 0.9220 (pptt) cc_final: 0.8961 (pptt) REVERT: C 267 MET cc_start: 0.8757 (tpp) cc_final: 0.8236 (mmp) REVERT: C 324 MET cc_start: 0.8720 (mmp) cc_final: 0.8409 (mmm) REVERT: C 402 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8625 (tp40) REVERT: C 405 ASN cc_start: 0.9257 (m110) cc_final: 0.8725 (m-40) REVERT: C 462 MET cc_start: 0.9043 (mmm) cc_final: 0.8774 (mmp) REVERT: D 436 ASN cc_start: 0.8835 (t0) cc_final: 0.8542 (t0) REVERT: E 324 MET cc_start: 0.8655 (mmp) cc_final: 0.8384 (mmp) REVERT: E 462 MET cc_start: 0.8999 (mmm) cc_final: 0.8412 (mmp) REVERT: F 324 MET cc_start: 0.8882 (mmp) cc_final: 0.8606 (mmp) REVERT: F 436 ASN cc_start: 0.8888 (t0) cc_final: 0.8629 (t0) REVERT: G 260 MET cc_start: 0.0513 (mmp) cc_final: 0.0156 (mmm) REVERT: I 267 MET cc_start: 0.9160 (tpp) cc_final: 0.8420 (tmm) REVERT: I 436 ASN cc_start: 0.8762 (t0) cc_final: 0.8476 (t0) REVERT: J 260 MET cc_start: 0.0972 (mmp) cc_final: 0.0006 (mmm) REVERT: J 267 MET cc_start: 0.9239 (tpp) cc_final: 0.8907 (mmm) REVERT: K 260 MET cc_start: 0.3477 (mpp) cc_final: 0.3171 (mmm) REVERT: K 324 MET cc_start: 0.8450 (mmp) cc_final: 0.7949 (mmm) REVERT: K 402 GLN cc_start: 0.8986 (tp-100) cc_final: 0.8748 (tm-30) REVERT: K 429 LYS cc_start: 0.9284 (pptt) cc_final: 0.9035 (pptt) REVERT: L 251 MET cc_start: 0.7042 (mtt) cc_final: 0.6785 (mtt) REVERT: L 267 MET cc_start: 0.9031 (tpp) cc_final: 0.8769 (mmm) outliers start: 6 outliers final: 0 residues processed: 329 average time/residue: 0.4402 time to fit residues: 238.1775 Evaluate side-chains 261 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 377 optimal weight: 20.0000 chunk 421 optimal weight: 9.9990 chunk 362 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 416 optimal weight: 10.0000 chunk 228 optimal weight: 50.0000 chunk 140 optimal weight: 40.0000 chunk 149 optimal weight: 10.0000 chunk 195 optimal weight: 220.0000 chunk 319 optimal weight: 30.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN D 405 ASN G 405 ASN ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.062285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.052292 restraints weight = 382177.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.053031 restraints weight = 290490.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.053533 restraints weight = 238313.870| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35268 Z= 0.142 Angle : 0.568 8.679 47556 Z= 0.310 Chirality : 0.039 0.150 5460 Planarity : 0.004 0.035 6552 Dihedral : 3.517 18.003 5064 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.11 % Allowed : 2.79 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.13), residues: 4668 helix: 2.77 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.95 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 397 HIS 0.002 0.001 HIS C 198 PHE 0.026 0.001 PHE A 411 TYR 0.008 0.001 TYR K 363 ARG 0.003 0.000 ARG G 220 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 2880) hydrogen bonds : angle 3.72925 ( 8532) covalent geometry : bond 0.00290 (35268) covalent geometry : angle 0.56794 (47556) *********************** 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 315 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 311 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.1092 (mmp) cc_final: 0.0804 (mmm) REVERT: A 267 MET cc_start: 0.9117 (tpp) cc_final: 0.8879 (mmm) REVERT: A 436 ASN cc_start: 0.8823 (t0) cc_final: 0.8582 (t0) REVERT: B 324 MET cc_start: 0.8446 (mmp) cc_final: 0.8203 (mmm) REVERT: B 405 ASN cc_start: 0.8871 (m-40) cc_final: 0.8617 (m-40) REVERT: C 267 MET cc_start: 0.8826 (tpp) cc_final: 0.8262 (mmm) REVERT: C 324 MET cc_start: 0.8874 (mmp) cc_final: 0.8528 (mmm) REVERT: C 402 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8820 (tp40) REVERT: C 405 ASN cc_start: 0.9192 (m110) cc_final: 0.8715 (m-40) REVERT: D 267 MET cc_start: 0.9049 (mmm) cc_final: 0.8794 (tpt) REVERT: D 436 ASN cc_start: 0.8806 (t0) cc_final: 0.8606 (t0) REVERT: E 324 MET cc_start: 0.8882 (mmp) cc_final: 0.8517 (mmp) REVERT: F 260 MET cc_start: 0.1154 (mmp) cc_final: 0.0711 (mmm) REVERT: F 324 MET cc_start: 0.9031 (mmp) cc_final: 0.8732 (mmm) REVERT: G 267 MET cc_start: 0.9116 (mmm) cc_final: 0.8696 (mmm) REVERT: H 251 MET cc_start: 0.7287 (mtm) cc_final: 0.6926 (mtp) REVERT: I 260 MET cc_start: 0.1061 (mmp) cc_final: 0.0350 (mmm) REVERT: K 324 MET cc_start: 0.8530 (mmp) cc_final: 0.8118 (mmm) outliers start: 4 outliers final: 0 residues processed: 314 average time/residue: 0.4387 time to fit residues: 229.5894 Evaluate side-chains 252 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 4.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 227 optimal weight: 9.9990 chunk 288 optimal weight: 30.0000 chunk 145 optimal weight: 0.4980 chunk 339 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 155 optimal weight: 30.0000 chunk 380 optimal weight: 7.9990 chunk 323 optimal weight: 40.0000 chunk 75 optimal weight: 10.0000 chunk 347 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN B 405 ASN K 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.062328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.052421 restraints weight = 380129.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.053182 restraints weight = 286097.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.053700 restraints weight = 233126.356| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 35268 Z= 0.112 Angle : 0.540 7.193 47556 Z= 0.290 Chirality : 0.037 0.146 5460 Planarity : 0.004 0.065 6552 Dihedral : 3.417 15.700 5064 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.13), residues: 4668 helix: 2.88 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.82 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 397 HIS 0.001 0.000 HIS K 198 PHE 0.032 0.001 PHE K 411 TYR 0.010 0.001 TYR K 363 ARG 0.002 0.000 ARG I 365 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 2880) hydrogen bonds : angle 3.53858 ( 8532) covalent geometry : bond 0.00225 (35268) covalent geometry : angle 0.54039 (47556) *********************** 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 317 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 315 time to evaluate : 3.737 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: 0.0974 (mmp) cc_final: 0.0681 (mmm) REVERT: B 405 ASN cc_start: 0.8984 (m110) cc_final: 0.8661 (m-40) REVERT: C 267 MET cc_start: 0.8835 (tpp) cc_final: 0.8215 (mmp) REVERT: C 324 MET cc_start: 0.8834 (mmp) cc_final: 0.8514 (mmm) REVERT: C 402 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8618 (tp40) REVERT: C 405 ASN cc_start: 0.9250 (m110) cc_final: 0.8615 (m-40) REVERT: D 251 MET cc_start: 0.7012 (mtt) cc_final: 0.6780 (mtt) REVERT: D 436 ASN cc_start: 0.8859 (t0) cc_final: 0.8565 (t0) REVERT: E 324 MET cc_start: 0.8819 (mmp) cc_final: 0.8459 (mmm) REVERT: F 251 MET cc_start: 0.7184 (mtm) cc_final: 0.6838 (mtp) REVERT: F 324 MET cc_start: 0.8956 (mmp) cc_final: 0.8733 (mmm) REVERT: G 267 MET cc_start: 0.9011 (mmm) cc_final: 0.8584 (mmp) REVERT: G 436 ASN cc_start: 0.8787 (t0) cc_final: 0.8586 (t0) REVERT: H 202 MET cc_start: 0.7236 (tmm) cc_final: 0.6720 (tmm) REVERT: H 267 MET cc_start: 0.9031 (mmm) cc_final: 0.8695 (tpt) REVERT: I 260 MET cc_start: 0.0876 (mmp) cc_final: 0.0310 (mmm) REVERT: K 324 MET cc_start: 0.8621 (mmp) cc_final: 0.8149 (mmm) REVERT: K 405 ASN cc_start: 0.8733 (m110) cc_final: 0.8511 (m-40) REVERT: L 436 ASN cc_start: 0.8599 (t0) cc_final: 0.8381 (t0) outliers start: 2 outliers final: 2 residues processed: 317 average time/residue: 0.4241 time to fit residues: 224.1442 Evaluate side-chains 251 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 440 optimal weight: 30.0000 chunk 238 optimal weight: 30.0000 chunk 124 optimal weight: 50.0000 chunk 431 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 302 optimal weight: 7.9990 chunk 380 optimal weight: 8.9990 chunk 373 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN C 149 ASN F 384 ASN K 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.061751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.051860 restraints weight = 383037.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052626 restraints weight = 287266.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.053142 restraints weight = 233063.620| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3227 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= 0.127 Angle : 0.566 7.420 47556 Z= 0.303 Chirality : 0.038 0.133 5460 Planarity : 0.004 0.050 6552 Dihedral : 3.439 16.685 5064 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.29 % Allowed : 2.30 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.13), residues: 4668 helix: 2.90 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.68 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 397 HIS 0.002 0.001 HIS B 198 PHE 0.022 0.001 PHE C 411 TYR 0.007 0.001 TYR K 363 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 2880) hydrogen bonds : angle 3.56955 ( 8532) covalent geometry : bond 0.00261 (35268) covalent geometry : angle 0.56626 (47556) *********************** 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 316 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 306 time to evaluate : 3.701 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: 0.0700 (mmp) cc_final: 0.0410 (mmm) REVERT: A 267 MET cc_start: 0.8860 (mmm) cc_final: 0.8650 (tmm) REVERT: A 403 ASP cc_start: 0.9002 (t70) cc_final: 0.8794 (t70) REVERT: B 324 MET cc_start: 0.8583 (mmp) cc_final: 0.8292 (mmm) REVERT: B 405 ASN cc_start: 0.8783 (m110) cc_final: 0.8563 (m-40) REVERT: C 202 MET cc_start: 0.7215 (tpp) cc_final: 0.7005 (tpp) REVERT: C 267 MET cc_start: 0.8876 (tpp) cc_final: 0.8270 (mmm) REVERT: C 324 MET cc_start: 0.8896 (mmp) cc_final: 0.8570 (mmm) REVERT: C 402 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8681 (tp40) REVERT: C 405 ASN cc_start: 0.9153 (m110) cc_final: 0.8540 (m110) REVERT: C 457 MET cc_start: 0.7995 (ppp) cc_final: 0.7650 (ppp) REVERT: D 436 ASN cc_start: 0.8857 (t0) cc_final: 0.8647 (t0) REVERT: E 324 MET cc_start: 0.8932 (mmp) cc_final: 0.8555 (mmm) REVERT: F 260 MET cc_start: 0.1077 (mmp) cc_final: 0.0147 (mmm) REVERT: F 384 ASN cc_start: 0.9534 (m-40) cc_final: 0.9303 (m110) REVERT: G 267 MET cc_start: 0.9087 (mmm) cc_final: 0.8740 (mmm) REVERT: G 324 MET cc_start: 0.8705 (mmp) cc_final: 0.8485 (mmm) REVERT: G 436 ASN cc_start: 0.8819 (t0) cc_final: 0.8551 (t0) REVERT: H 260 MET cc_start: -0.0296 (mmm) cc_final: -0.0761 (mmm) REVERT: I 260 MET cc_start: 0.0859 (mmp) cc_final: 0.0331 (mmm) REVERT: I 267 MET cc_start: 0.9229 (tpp) cc_final: 0.8984 (tmm) REVERT: K 324 MET cc_start: 0.8773 (mmp) cc_final: 0.8200 (mmm) REVERT: K 405 ASN cc_start: 0.8728 (m110) cc_final: 0.8495 (m-40) REVERT: L 436 ASN cc_start: 0.8598 (t0) cc_final: 0.8395 (t0) outliers start: 10 outliers final: 5 residues processed: 316 average time/residue: 0.4264 time to fit residues: 224.0653 Evaluate side-chains 265 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 260 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 216 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 466 optimal weight: 8.9990 chunk 388 optimal weight: 40.0000 chunk 457 optimal weight: 50.0000 chunk 382 optimal weight: 30.0000 chunk 354 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 403 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 404 optimal weight: 30.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 277 GLN ** K 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 = 0.3653 r_free = 0.3653 target = 0.061357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.051524 restraints weight = 381520.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.052256 restraints weight = 286338.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.052769 restraints weight = 233463.266| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35268 Z= 0.128 Angle : 0.576 9.637 47556 Z= 0.307 Chirality : 0.038 0.141 5460 Planarity : 0.004 0.052 6552 Dihedral : 3.472 16.850 5064 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.13), residues: 4668 helix: 2.87 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.56 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 397 HIS 0.001 0.001 HIS B 198 PHE 0.017 0.001 PHE I 411 TYR 0.007 0.001 TYR J 363 ARG 0.003 0.000 ARG I 365 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 2880) hydrogen bonds : angle 3.62249 ( 8532) covalent geometry : bond 0.00267 (35268) covalent geometry : angle 0.57638 (47556) *********************** 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 309 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 4.286 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: A 260 MET cc_start: 0.0755 (mmp) cc_final: 0.0431 (mmm) REVERT: A 436 ASN cc_start: 0.8825 (t0) cc_final: 0.8623 (t0) REVERT: B 324 MET cc_start: 0.8605 (mmp) cc_final: 0.8225 (mmm) REVERT: B 405 ASN cc_start: 0.8856 (m110) cc_final: 0.8589 (m-40) REVERT: C 267 MET cc_start: 0.8876 (tpp) cc_final: 0.8318 (mmm) REVERT: C 324 MET cc_start: 0.8968 (mmp) cc_final: 0.8679 (mmm) REVERT: C 402 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8654 (tm-30) REVERT: C 405 ASN cc_start: 0.9255 (m110) cc_final: 0.8663 (m-40) REVERT: C 457 MET cc_start: 0.8074 (ppp) cc_final: 0.7743 (ppp) REVERT: D 251 MET cc_start: 0.7561 (mtt) cc_final: 0.6634 (mtt) REVERT: D 324 MET cc_start: 0.8799 (mmp) cc_final: 0.8584 (mmm) REVERT: E 324 MET cc_start: 0.8933 (mmp) cc_final: 0.8572 (mmm) REVERT: F 267 MET cc_start: 0.9236 (tpp) cc_final: 0.8508 (tpt) REVERT: F 324 MET cc_start: 0.8907 (mmm) cc_final: 0.8379 (mmm) REVERT: G 324 MET cc_start: 0.8801 (mmp) cc_final: 0.8530 (mmp) REVERT: I 260 MET cc_start: 0.1195 (mmp) cc_final: 0.0656 (mmm) REVERT: J 251 MET cc_start: 0.7047 (mtt) cc_final: 0.6693 (mtm) REVERT: J 260 MET cc_start: 0.0167 (mmm) cc_final: -0.0062 (mmm) REVERT: K 267 MET cc_start: 0.9102 (mmm) cc_final: 0.8787 (mmm) REVERT: K 324 MET cc_start: 0.8696 (mmp) cc_final: 0.8289 (mmm) REVERT: L 260 MET cc_start: 0.0121 (mmm) cc_final: -0.0105 (mmm) REVERT: L 267 MET cc_start: 0.9034 (mmm) cc_final: 0.8623 (tpt) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.4676 time to fit residues: 242.6291 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 : 4.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 197 optimal weight: 50.0000 chunk 140 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 177 optimal weight: 50.0000 chunk 442 optimal weight: 4.9990 chunk 402 optimal weight: 50.0000 chunk 78 optimal weight: 90.0000 chunk 441 optimal weight: 10.0000 overall best weight: 4.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.061562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.051759 restraints weight = 382614.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.052503 restraints weight = 285679.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.053023 restraints weight = 232366.314| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 35268 Z= 0.113 Angle : 0.572 7.946 47556 Z= 0.302 Chirality : 0.038 0.150 5460 Planarity : 0.004 0.053 6552 Dihedral : 3.384 15.768 5064 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.09 % Allowed : 0.72 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.13), residues: 4668 helix: 2.93 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.37 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 397 HIS 0.001 0.000 HIS B 198 PHE 0.017 0.001 PHE H 411 TYR 0.023 0.001 TYR F 240 ARG 0.002 0.000 ARG H 365 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 2880) hydrogen bonds : angle 3.51748 ( 8532) covalent geometry : bond 0.00231 (35268) covalent geometry : angle 0.57198 (47556) *********************** 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 309 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 4.237 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 251 MET cc_start: 0.6903 (mtm) cc_final: 0.6664 (mtp) REVERT: A 260 MET cc_start: 0.0638 (mmp) cc_final: 0.0357 (mmm) REVERT: A 267 MET cc_start: 0.8888 (mmm) cc_final: 0.8619 (mmm) REVERT: A 384 ASN cc_start: 0.8944 (p0) cc_final: 0.8577 (p0) REVERT: A 436 ASN cc_start: 0.8785 (t0) cc_final: 0.8507 (t0) REVERT: B 324 MET cc_start: 0.8585 (mmp) cc_final: 0.8323 (mmm) REVERT: B 405 ASN cc_start: 0.8868 (m110) cc_final: 0.8446 (m-40) REVERT: C 267 MET cc_start: 0.8853 (tpp) cc_final: 0.8320 (mmm) REVERT: C 324 MET cc_start: 0.8908 (mmp) cc_final: 0.8706 (mmm) REVERT: C 402 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8728 (tm-30) REVERT: C 405 ASN cc_start: 0.9239 (m110) cc_final: 0.8667 (m-40) REVERT: C 457 MET cc_start: 0.8010 (ppp) cc_final: 0.7746 (ppp) REVERT: D 260 MET cc_start: 0.0002 (mmm) cc_final: -0.0201 (mmm) REVERT: D 324 MET cc_start: 0.8832 (mmp) cc_final: 0.8601 (mmp) REVERT: D 384 ASN cc_start: 0.8887 (p0) cc_final: 0.8467 (p0) REVERT: D 436 ASN cc_start: 0.8843 (t0) cc_final: 0.8576 (t0) REVERT: E 324 MET cc_start: 0.8947 (mmm) cc_final: 0.8482 (mmp) REVERT: E 436 ASN cc_start: 0.8675 (t0) cc_final: 0.8470 (t0) REVERT: F 324 MET cc_start: 0.8826 (mmm) cc_final: 0.8351 (mmm) REVERT: G 267 MET cc_start: 0.9042 (mmm) cc_final: 0.8644 (mmm) REVERT: G 324 MET cc_start: 0.8820 (mmp) cc_final: 0.8564 (mmp) REVERT: H 324 MET cc_start: 0.8770 (mmp) cc_final: 0.8548 (mmm) REVERT: H 436 ASN cc_start: 0.8514 (t0) cc_final: 0.8277 (t0) REVERT: I 260 MET cc_start: 0.0955 (mmp) cc_final: 0.0463 (mmm) REVERT: I 324 MET cc_start: 0.8758 (mmp) cc_final: 0.8530 (mmm) REVERT: K 202 MET cc_start: 0.6899 (tpp) cc_final: 0.6628 (tpp) REVERT: K 267 MET cc_start: 0.9083 (mmm) cc_final: 0.8765 (mmm) REVERT: K 324 MET cc_start: 0.9031 (mmm) cc_final: 0.8279 (mmm) REVERT: L 260 MET cc_start: 0.0262 (mmm) cc_final: 0.0044 (mmm) REVERT: L 267 MET cc_start: 0.8891 (mmm) cc_final: 0.8625 (tpt) REVERT: L 436 ASN cc_start: 0.8624 (t0) cc_final: 0.8377 (t0) outliers start: 3 outliers final: 2 residues processed: 309 average time/residue: 0.4500 time to fit residues: 232.1265 Evaluate side-chains 260 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 289 optimal weight: 30.0000 chunk 57 optimal weight: 30.0000 chunk 161 optimal weight: 50.0000 chunk 249 optimal weight: 50.0000 chunk 189 optimal weight: 30.0000 chunk 460 optimal weight: 0.9980 chunk 11 optimal weight: 40.0000 chunk 217 optimal weight: 6.9990 chunk 439 optimal weight: 50.0000 chunk 251 optimal weight: 30.0000 chunk 199 optimal weight: 50.0000 overall best weight: 19.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN ** E 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 490 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.059190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.049420 restraints weight = 384293.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.050137 restraints weight = 285797.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.050638 restraints weight = 232037.110| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35268 Z= 0.232 Angle : 0.707 10.472 47556 Z= 0.388 Chirality : 0.041 0.170 5460 Planarity : 0.005 0.052 6552 Dihedral : 4.139 21.972 5064 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.98 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.12), residues: 4668 helix: 2.20 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.87 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 397 HIS 0.006 0.002 HIS B 198 PHE 0.031 0.002 PHE I 411 TYR 0.014 0.002 TYR F 240 ARG 0.009 0.001 ARG K 357 Details of bonding type rmsd hydrogen bonds : bond 0.04873 ( 2880) hydrogen bonds : angle 4.33001 ( 8532) covalent geometry : bond 0.00476 (35268) covalent geometry : angle 0.70729 (47556) *********************** 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 259 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 3.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6772 (mtm) cc_final: 0.6350 (mtp) REVERT: A 260 MET cc_start: 0.0889 (mmp) cc_final: 0.0671 (mmm) REVERT: A 267 MET cc_start: 0.9106 (mmm) cc_final: 0.8840 (mmm) REVERT: A 324 MET cc_start: 0.8832 (mmp) cc_final: 0.8586 (mmm) REVERT: B 202 MET cc_start: 0.7175 (tpt) cc_final: 0.6816 (tpp) REVERT: B 324 MET cc_start: 0.8845 (mmp) cc_final: 0.8439 (mmm) REVERT: B 405 ASN cc_start: 0.9004 (m110) cc_final: 0.8515 (m110) REVERT: C 267 MET cc_start: 0.9012 (tpp) cc_final: 0.8504 (mmm) REVERT: C 324 MET cc_start: 0.9222 (mmm) cc_final: 0.8705 (mmm) REVERT: C 402 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8586 (tp40) REVERT: C 405 ASN cc_start: 0.9200 (m-40) cc_final: 0.8496 (m-40) REVERT: D 267 MET cc_start: 0.9305 (mmm) cc_final: 0.9045 (mmm) REVERT: D 324 MET cc_start: 0.8936 (mmp) cc_final: 0.8644 (mmm) REVERT: E 267 MET cc_start: 0.9197 (mmm) cc_final: 0.8820 (tpt) REVERT: E 324 MET cc_start: 0.9026 (mmm) cc_final: 0.8604 (mmm) REVERT: E 462 MET cc_start: 0.9238 (mmm) cc_final: 0.8784 (mmp) REVERT: F 267 MET cc_start: 0.9249 (tpp) cc_final: 0.8472 (tpt) REVERT: F 324 MET cc_start: 0.8894 (mmm) cc_final: 0.8416 (mmm) REVERT: G 267 MET cc_start: 0.9264 (mmm) cc_final: 0.8920 (mmm) REVERT: G 324 MET cc_start: 0.9034 (mmp) cc_final: 0.8647 (mmm) REVERT: H 324 MET cc_start: 0.9040 (mmp) cc_final: 0.8670 (mmp) REVERT: H 462 MET cc_start: 0.9127 (mmm) cc_final: 0.8714 (mmp) REVERT: I 260 MET cc_start: 0.1321 (mmp) cc_final: 0.0809 (mmm) REVERT: I 324 MET cc_start: 0.8821 (mmp) cc_final: 0.8586 (mmm) REVERT: J 267 MET cc_start: 0.9216 (tpp) cc_final: 0.8307 (tpt) REVERT: K 267 MET cc_start: 0.9080 (mmm) cc_final: 0.8837 (mmm) REVERT: K 324 MET cc_start: 0.9164 (mmm) cc_final: 0.8463 (mmm) REVERT: L 324 MET cc_start: 0.8701 (mmp) cc_final: 0.8500 (mmm) REVERT: L 462 MET cc_start: 0.9138 (mmm) cc_final: 0.8668 (mmp) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.4488 time to fit residues: 194.7050 Evaluate side-chains 220 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 4.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 209 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 293 optimal weight: 8.9990 chunk 399 optimal weight: 6.9990 chunk 362 optimal weight: 30.0000 chunk 380 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 338 optimal weight: 8.9990 chunk 205 optimal weight: 40.0000 chunk 245 optimal weight: 8.9990 chunk 319 optimal weight: 50.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.059830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.050155 restraints weight = 383233.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.050890 restraints weight = 284401.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.051385 restraints weight = 230667.096| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35268 Z= 0.139 Angle : 0.614 9.000 47556 Z= 0.326 Chirality : 0.039 0.144 5460 Planarity : 0.004 0.053 6552 Dihedral : 3.773 17.677 5064 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.28 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.13), residues: 4668 helix: 2.55 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.70 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 397 HIS 0.002 0.001 HIS L 198 PHE 0.024 0.002 PHE B 411 TYR 0.015 0.002 TYR F 240 ARG 0.003 0.000 ARG H 365 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 2880) hydrogen bonds : angle 3.90209 ( 8532) covalent geometry : bond 0.00292 (35268) covalent geometry : angle 0.61383 (47556) *********************** 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 278 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 4.052 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 251 MET cc_start: 0.6781 (mtm) cc_final: 0.6408 (mtp) REVERT: A 260 MET cc_start: 0.0945 (mmp) cc_final: 0.0639 (mmm) REVERT: A 267 MET cc_start: 0.9050 (mmm) cc_final: 0.8816 (mmm) REVERT: A 324 MET cc_start: 0.8830 (mmp) cc_final: 0.8543 (mmm) REVERT: B 324 MET cc_start: 0.8830 (mmp) cc_final: 0.8394 (mmm) REVERT: B 405 ASN cc_start: 0.9044 (m110) cc_final: 0.8545 (m110) REVERT: B 457 MET cc_start: 0.8519 (ppp) cc_final: 0.8202 (ppp) REVERT: C 267 MET cc_start: 0.9098 (tpp) cc_final: 0.8543 (mmm) REVERT: C 270 MET cc_start: 0.8179 (tpt) cc_final: 0.7605 (mpp) REVERT: C 324 MET cc_start: 0.9134 (mmm) cc_final: 0.8558 (mmm) REVERT: C 402 GLN cc_start: 0.9137 (tp-100) cc_final: 0.8683 (tm-30) REVERT: C 405 ASN cc_start: 0.9266 (m-40) cc_final: 0.8732 (m110) REVERT: C 457 MET cc_start: 0.8293 (ppp) cc_final: 0.7804 (ppp) REVERT: D 267 MET cc_start: 0.9141 (mmm) cc_final: 0.8897 (mmp) REVERT: D 324 MET cc_start: 0.8945 (mmp) cc_final: 0.8579 (mmm) REVERT: E 324 MET cc_start: 0.8969 (mmm) cc_final: 0.8559 (mmm) REVERT: E 405 ASN cc_start: 0.9097 (m110) cc_final: 0.8565 (m110) REVERT: F 267 MET cc_start: 0.9164 (tpp) cc_final: 0.8437 (tpt) REVERT: F 324 MET cc_start: 0.8855 (mmm) cc_final: 0.8330 (mmm) REVERT: G 267 MET cc_start: 0.9186 (mmm) cc_final: 0.8832 (mmm) REVERT: G 324 MET cc_start: 0.9012 (mmp) cc_final: 0.8685 (mmm) REVERT: H 260 MET cc_start: 0.0911 (mmp) cc_final: 0.0678 (mmm) REVERT: H 324 MET cc_start: 0.8999 (mmp) cc_final: 0.8671 (mmp) REVERT: I 324 MET cc_start: 0.8793 (mmp) cc_final: 0.8494 (mmm) REVERT: K 267 MET cc_start: 0.9026 (mmm) cc_final: 0.8753 (mmm) REVERT: K 324 MET cc_start: 0.9095 (mmm) cc_final: 0.8517 (mmm) REVERT: K 405 ASN cc_start: 0.8877 (m110) cc_final: 0.8496 (m-40) REVERT: L 324 MET cc_start: 0.8646 (mmp) cc_final: 0.8428 (mmm) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.6436 time to fit residues: 300.1185 Evaluate side-chains 239 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 5.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 298 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 343 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 chunk 452 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 389 optimal weight: 8.9990 chunk 317 optimal weight: 40.0000 chunk 415 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 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** ** 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** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.060071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.050456 restraints weight = 381274.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.051194 restraints weight = 283677.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.051696 restraints weight = 230359.525| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35268 Z= 0.133 Angle : 0.609 9.221 47556 Z= 0.323 Chirality : 0.039 0.187 5460 Planarity : 0.004 0.054 6552 Dihedral : 3.625 17.502 5064 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.71 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.13), residues: 4668 helix: 2.66 (0.08), residues: 3624 sheet: None (None), residues: 0 loop : -1.63 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 397 HIS 0.002 0.001 HIS L 198 PHE 0.026 0.002 PHE H 411 TYR 0.020 0.002 TYR I 240 ARG 0.003 0.000 ARG B 365 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 2880) hydrogen bonds : angle 3.78094 ( 8532) covalent geometry : bond 0.00278 (35268) covalent geometry : angle 0.60926 (47556) ********************** 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 290 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 4.424 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: A 251 MET cc_start: 0.6718 (mtm) cc_final: 0.6343 (mtp) REVERT: A 260 MET cc_start: 0.0958 (mmp) cc_final: 0.0642 (mmm) REVERT: A 267 MET cc_start: 0.9040 (mmm) cc_final: 0.8771 (mmm) REVERT: A 324 MET cc_start: 0.8833 (mmp) cc_final: 0.8531 (mmm) REVERT: B 405 ASN cc_start: 0.9115 (m110) cc_final: 0.8600 (m110) REVERT: C 267 MET cc_start: 0.9118 (tpp) cc_final: 0.8435 (mmm) REVERT: C 324 MET cc_start: 0.9128 (mmm) cc_final: 0.8478 (mmm) REVERT: C 402 GLN cc_start: 0.9168 (tp-100) cc_final: 0.8721 (tm-30) REVERT: C 405 ASN cc_start: 0.9250 (m-40) cc_final: 0.8705 (m110) REVERT: C 457 MET cc_start: 0.8268 (ppp) cc_final: 0.7807 (ppp) REVERT: D 267 MET cc_start: 0.9216 (mmm) cc_final: 0.8933 (mmp) REVERT: D 324 MET cc_start: 0.8986 (mmp) cc_final: 0.8597 (mmm) REVERT: E 324 MET cc_start: 0.9014 (mmm) cc_final: 0.8596 (mmm) REVERT: E 405 ASN cc_start: 0.9071 (m110) cc_final: 0.8547 (m110) REVERT: F 267 MET cc_start: 0.9153 (tpp) cc_final: 0.8396 (tpt) REVERT: F 324 MET cc_start: 0.8900 (mmm) cc_final: 0.8396 (mmm) REVERT: G 324 MET cc_start: 0.9039 (mmp) cc_final: 0.8708 (mmm) REVERT: H 324 MET cc_start: 0.9036 (mmp) cc_final: 0.8648 (mmp) REVERT: I 267 MET cc_start: 0.9155 (mmp) cc_final: 0.8676 (mmp) REVERT: I 324 MET cc_start: 0.8869 (mmp) cc_final: 0.8518 (mmm) REVERT: J 324 MET cc_start: 0.8710 (mmp) cc_final: 0.8506 (mmm) REVERT: J 405 ASN cc_start: 0.9088 (m110) cc_final: 0.8604 (m-40) REVERT: K 202 MET cc_start: 0.7439 (tpp) cc_final: 0.7149 (tpp) REVERT: K 267 MET cc_start: 0.9056 (mmm) cc_final: 0.8776 (mmm) REVERT: K 304 LEU cc_start: 0.9130 (tt) cc_final: 0.8859 (mt) REVERT: K 324 MET cc_start: 0.9080 (mmm) cc_final: 0.8529 (mmm) REVERT: L 324 MET cc_start: 0.8662 (mmp) cc_final: 0.8406 (mmm) REVERT: L 405 ASN cc_start: 0.9082 (m110) cc_final: 0.8578 (m110) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.4546 time to fit residues: 219.2539 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 : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 353 optimal weight: 20.0000 chunk 418 optimal weight: 0.0000 chunk 208 optimal weight: 5.9990 chunk 300 optimal weight: 0.2980 chunk 368 optimal weight: 20.0000 chunk 67 optimal weight: 50.0000 chunk 350 optimal weight: 50.0000 chunk 169 optimal weight: 30.0000 chunk 276 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 332 optimal weight: 50.0000 overall best weight: 4.4590 ------------------------------------------------------------------------------- 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** ** G 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.060534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.050905 restraints weight = 383540.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.051671 restraints weight = 285311.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.052181 restraints weight = 230359.062| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5045 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= 0.119 Angle : 0.611 11.443 47556 Z= 0.316 Chirality : 0.039 0.208 5460 Planarity : 0.004 0.055 6552 Dihedral : 3.502 18.488 5064 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.13), residues: 4668 helix: 2.82 (0.08), residues: 3624 sheet: None (None), residues: 0 loop : -1.52 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 397 HIS 0.001 0.000 HIS L 198 PHE 0.036 0.001 PHE K 411 TYR 0.008 0.001 TYR E 240 ARG 0.003 0.000 ARG F 365 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 2880) hydrogen bonds : angle 3.60459 ( 8532) covalent geometry : bond 0.00242 (35268) covalent geometry : angle 0.61144 (47556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11586.66 seconds wall clock time: 206 minutes 5.11 seconds (12365.11 seconds total)