Starting phenix.real_space_refine on Fri Aug 7 21:57:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21fh_67625/08_2026/21fh_67625.cif Found real_map, /net/cci-nas-00/data/ceres_data/21fh_67625/08_2026/21fh_67625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21fh_67625/08_2026/21fh_67625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21fh_67625/08_2026/21fh_67625.map" model { file = "/net/cci-nas-00/data/ceres_data/21fh_67625/08_2026/21fh_67625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21fh_67625/08_2026/21fh_67625.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 63 5.16 5 Na 6 4.78 5 C 7788 2.51 5 N 1755 2.21 5 O 1998 1.98 5 H 11853 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23463 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7818 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 20, 'TRANS': 479} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C Time building chain proxies: 7.98, per 1000 atoms: 0.34 Number of scatterers: 23463 At special positions: 0 Unit cell: (114.46, 120.28, 79.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 Na 6 11.00 O 1998 8.00 N 1755 7.00 C 7788 6.00 H 11853 1.00 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: 2.12 Conformation dependent library (CDL) restraints added in 762.9 milliseconds 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 7 through 28 removed outlier: 3.507A pdb=" N PHE A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Proline residue: A 24 - end of helix Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 48 through 67 removed outlier: 3.798A pdb=" N LEU A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.540A pdb=" N LYS A 72 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 101 through 109 removed outlier: 4.005A pdb=" N THR A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.767A pdb=" N TYR A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 removed outlier: 3.804A pdb=" N ALA A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.693A pdb=" N PHE A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 4.031A pdb=" N ILE A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.580A pdb=" N CYS A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 183 through 209 removed outlier: 3.801A pdb=" N THR A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.571A pdb=" N ALA A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 247 removed outlier: 3.523A pdb=" N THR A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 274 removed outlier: 3.592A pdb=" N SER A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 293 removed outlier: 3.533A pdb=" N THR A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 308 through 324 removed outlier: 5.066A pdb=" N VAL A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 324 " --> pdb=" O TRP A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 340 through 373 removed outlier: 3.639A pdb=" N GLY A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 removed outlier: 3.755A pdb=" N GLU A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 431 removed outlier: 4.068A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 463 removed outlier: 3.839A pdb=" N LEU A 453 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Proline residue: A 457 - end of helix removed outlier: 3.940A pdb=" N LEU A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 477 through 498 removed outlier: 3.768A pdb=" N PHE A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 498 " --> pdb=" O LYS A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 removed outlier: 3.507A pdb=" N PHE B 11 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Proline residue: B 24 - end of helix Processing helix chain 'B' and resid 28 through 47 Processing helix chain 'B' and resid 48 through 67 removed outlier: 3.799A pdb=" N LEU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 removed outlier: 3.540A pdb=" N LYS B 72 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 101 through 109 removed outlier: 4.005A pdb=" N THR B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 removed outlier: 3.767A pdb=" N TYR B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 removed outlier: 3.804A pdb=" N ALA B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.693A pdb=" N PHE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 161 removed outlier: 4.031A pdb=" N ILE B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.581A pdb=" N CYS B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 183 through 209 removed outlier: 3.801A pdb=" N THR B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.571A pdb=" N ALA B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 247 removed outlier: 3.523A pdb=" N THR B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 274 removed outlier: 3.592A pdb=" N SER B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 293 removed outlier: 3.533A pdb=" N THR B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 308 through 324 removed outlier: 5.067A pdb=" N VAL B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 324 " --> pdb=" O TRP B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'B' and resid 340 through 373 removed outlier: 3.639A pdb=" N GLY B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 385 removed outlier: 3.754A pdb=" N GLU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 Processing helix chain 'B' and resid 400 through 431 removed outlier: 4.067A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 431 " --> pdb=" O MET B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 463 removed outlier: 3.839A pdb=" N LEU B 453 " --> pdb=" O TRP B 449 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 457 - end of helix removed outlier: 3.940A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 477 through 498 removed outlier: 3.768A pdb=" N PHE B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 498 " --> pdb=" O LYS B 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 28 removed outlier: 3.506A pdb=" N PHE C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE C 15 " --> pdb=" O PHE C 11 " (cutoff:3.500A) Proline residue: C 24 - end of helix Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 48 through 67 removed outlier: 3.798A pdb=" N LEU C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.540A pdb=" N LYS C 72 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 98 Processing helix chain 'C' and resid 101 through 109 removed outlier: 4.005A pdb=" N THR C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 116 removed outlier: 3.767A pdb=" N TYR C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 removed outlier: 3.804A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.693A pdb=" N PHE C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 removed outlier: 4.031A pdb=" N ILE C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 removed outlier: 3.581A pdb=" N CYS C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 179 through 182 Processing helix chain 'C' and resid 183 through 209 removed outlier: 3.801A pdb=" N THR C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.572A pdb=" N ALA C 213 " --> pdb=" O THR C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 247 removed outlier: 3.523A pdb=" N THR C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 274 removed outlier: 3.592A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 293 removed outlier: 3.534A pdb=" N THR C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 308 through 324 removed outlier: 5.066A pdb=" N VAL C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 324 " --> pdb=" O TRP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 340 through 373 removed outlier: 3.639A pdb=" N GLY C 347 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 removed outlier: 3.754A pdb=" N GLU C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 396 Processing helix chain 'C' and resid 400 through 431 removed outlier: 4.067A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR C 431 " --> pdb=" O MET C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 463 removed outlier: 3.839A pdb=" N LEU C 453 " --> pdb=" O TRP C 449 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Proline residue: C 457 - end of helix removed outlier: 3.940A pdb=" N LEU C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 476 No H-bonds generated for 'chain 'C' and resid 474 through 476' Processing helix chain 'C' and resid 477 through 498 removed outlier: 3.768A pdb=" N PHE C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR C 498 " --> pdb=" O LYS C 494 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2403 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: 5.04 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.01: 11835 1.01 - 1.21: 30 1.21 - 1.41: 4908 1.41 - 1.61: 6912 1.61 - 1.81: 108 Bond restraints: 23793 Sorted by residual: bond pdb=" NZ LYS C 374 " pdb=" HZ2 LYS C 374 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" NZ LYS B 374 " pdb=" HZ2 LYS B 374 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" NZ LYS A 374 " pdb=" HZ2 LYS A 374 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" NZ LYS A 374 " pdb=" HZ3 LYS A 374 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" NZ LYS B 374 " pdb=" HZ3 LYS B 374 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 23788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.39: 43086 5.39 - 10.78: 21 10.78 - 16.18: 3 16.18 - 21.57: 0 21.57 - 26.96: 9 Bond angle restraints: 43119 Sorted by residual: angle pdb=" CG2 THR C 419 " pdb=" CB THR C 419 " pdb=" HB THR C 419 " ideal model delta sigma weight residual 108.00 81.04 26.96 3.00e+00 1.11e-01 8.08e+01 angle pdb=" CG2 THR A 419 " pdb=" CB THR A 419 " pdb=" HB THR A 419 " ideal model delta sigma weight residual 108.00 81.06 26.94 3.00e+00 1.11e-01 8.06e+01 angle pdb=" CG2 THR B 419 " pdb=" CB THR B 419 " pdb=" HB THR B 419 " ideal model delta sigma weight residual 108.00 81.06 26.94 3.00e+00 1.11e-01 8.06e+01 angle pdb=" OG1 THR B 419 " pdb=" CB THR B 419 " pdb=" HB THR B 419 " ideal model delta sigma weight residual 109.00 82.75 26.25 3.00e+00 1.11e-01 7.66e+01 angle pdb=" OG1 THR A 419 " pdb=" CB THR A 419 " pdb=" HB THR A 419 " ideal model delta sigma weight residual 109.00 82.78 26.22 3.00e+00 1.11e-01 7.64e+01 ... (remaining 43114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 9756 15.87 - 31.75: 940 31.75 - 47.62: 280 47.62 - 63.49: 217 63.49 - 79.36: 21 Dihedral angle restraints: 11214 sinusoidal: 5817 harmonic: 5397 Sorted by residual: dihedral pdb=" C LYS C 374 " pdb=" N LYS C 374 " pdb=" CA LYS C 374 " pdb=" CB LYS C 374 " ideal model delta harmonic sigma weight residual -122.60 -134.73 12.13 0 2.50e+00 1.60e-01 2.36e+01 dihedral pdb=" C LYS A 374 " pdb=" N LYS A 374 " pdb=" CA LYS A 374 " pdb=" CB LYS A 374 " ideal model delta harmonic sigma weight residual -122.60 -134.70 12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" C LYS B 374 " pdb=" N LYS B 374 " pdb=" CA LYS B 374 " pdb=" CB LYS B 374 " ideal model delta harmonic sigma weight residual -122.60 -134.70 12.10 0 2.50e+00 1.60e-01 2.34e+01 ... (remaining 11211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 1902 0.279 - 0.559: 3 0.559 - 0.838: 0 0.838 - 1.118: 0 1.118 - 1.397: 3 Chirality restraints: 1908 Sorted by residual: chirality pdb=" CB THR C 419 " pdb=" CA THR C 419 " pdb=" OG1 THR C 419 " pdb=" CG2 THR C 419 " both_signs ideal model delta sigma weight residual False 2.55 1.15 1.40 2.00e-01 2.50e+01 4.88e+01 chirality pdb=" CB THR A 419 " pdb=" CA THR A 419 " pdb=" OG1 THR A 419 " pdb=" CG2 THR A 419 " both_signs ideal model delta sigma weight residual False 2.55 1.15 1.40 2.00e-01 2.50e+01 4.88e+01 chirality pdb=" CB THR B 419 " pdb=" CA THR B 419 " pdb=" OG1 THR B 419 " pdb=" CG2 THR B 419 " both_signs ideal model delta sigma weight residual False 2.55 1.16 1.40 2.00e-01 2.50e+01 4.87e+01 ... (remaining 1905 not shown) Planarity restraints: 3384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 251 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C GLY A 251 " 0.034 2.00e-02 2.50e+03 pdb=" O GLY A 251 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 252 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 251 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C GLY C 251 " 0.034 2.00e-02 2.50e+03 pdb=" O GLY C 251 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU C 252 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 251 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C GLY B 251 " 0.034 2.00e-02 2.50e+03 pdb=" O GLY B 251 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU B 252 " -0.011 2.00e-02 2.50e+03 ... (remaining 3381 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2102 2.24 - 2.83: 50492 2.83 - 3.42: 59614 3.42 - 4.01: 81546 4.01 - 4.60: 126643 Nonbonded interactions: 320397 Sorted by model distance: nonbonded pdb=" O ASN A 503 " pdb="HD21 ASN A 503 " model vdw 1.653 2.450 nonbonded pdb=" O ASN B 503 " pdb="HD21 ASN B 503 " model vdw 1.653 2.450 nonbonded pdb=" O ASN C 503 " pdb="HD21 ASN C 503 " model vdw 1.654 2.450 nonbonded pdb=" OD1 ASP B 421 " pdb=" H SER B 422 " model vdw 1.697 2.450 nonbonded pdb=" OD1 ASP C 421 " pdb=" H SER C 422 " model vdw 1.698 2.450 ... (remaining 320392 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.130 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 25.350 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.003 0.040 11940 Z= 0.181 Angle : 0.645 10.985 16284 Z= 0.404 Chirality : 0.069 1.397 1908 Planarity : 0.005 0.048 1947 Dihedral : 15.906 79.364 4029 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.22 % Allowed : 16.06 % Favored : 82.73 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1494 helix: 1.08 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -0.96 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 342 TYR 0.012 0.001 TYR A 104 PHE 0.020 0.001 PHE A 240 TRP 0.008 0.001 TRP C 321 HIS 0.002 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.18 (11940) covalent geometry : angle 0.64500 / 0.40 (16284) hydrogen bonds : bond 0.20524 / 13.32 ( 810) hydrogen bonds : angle 5.53379 / 3.99 ( 2403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: B 81 LYS cc_start: 0.7554 (ttpp) cc_final: 0.7109 (pptt) REVERT: B 194 MET cc_start: 0.8093 (mmt) cc_final: 0.7878 (mmt) REVERT: B 392 MET cc_start: 0.8584 (mmt) cc_final: 0.7858 (mmp) REVERT: B 468 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6456 (mmmt) REVERT: C 81 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7119 (pptt) REVERT: C 368 MET cc_start: 0.8811 (ttm) cc_final: 0.8562 (ttm) REVERT: C 468 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6762 (mmmt) outliers start: 15 outliers final: 7 residues processed: 159 average time/residue: 0.8727 time to fit residues: 156.4953 Evaluate side-chains 138 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 468 LYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 468 LYS Chi-restraints excluded: chain C residue 472 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN A 503 ASN B 86 ASN B 503 ASN C 86 ASN C 503 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.110650 restraints weight = 33777.735| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.53 r_work: 0.3155 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11940 Z= 0.171 Angle : 0.606 10.866 16284 Z= 0.341 Chirality : 0.067 1.394 1908 Planarity : 0.005 0.049 1947 Dihedral : 4.808 47.094 1595 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.76 % Allowed : 14.52 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.22), residues: 1494 helix: 1.27 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -1.19 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 296 TYR 0.015 0.002 TYR C 104 PHE 0.024 0.002 PHE B 240 TRP 0.010 0.002 TRP B 110 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (11940) covalent geometry : angle 0.60642 / 0.34 (16284) hydrogen bonds : bond 0.08272 / 5.44 ( 810) hydrogen bonds : angle 4.25596 / 3.12 ( 2403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.7395 (ttpp) cc_final: 0.6567 (pptt) REVERT: B 392 MET cc_start: 0.8227 (mmt) cc_final: 0.7396 (mmp) REVERT: B 468 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6019 (mmmt) REVERT: C 81 LYS cc_start: 0.7527 (ttpp) cc_final: 0.6647 (pptt) REVERT: C 311 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: C 375 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7872 (mt-10) REVERT: C 468 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6375 (mmmt) outliers start: 34 outliers final: 14 residues processed: 160 average time/residue: 0.8053 time to fit residues: 145.9845 Evaluate side-chains 145 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 468 LYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 468 LYS Chi-restraints excluded: chain C residue 472 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 ASN C 503 ASN 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 = 0.141853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109938 restraints weight = 33833.405| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.51 r_work: 0.3124 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11940 Z= 0.158 Angle : 0.581 10.927 16284 Z= 0.325 Chirality : 0.067 1.414 1908 Planarity : 0.005 0.050 1947 Dihedral : 4.675 46.394 1592 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.35 % Allowed : 14.76 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.22), residues: 1494 helix: 1.39 (0.15), residues: 1191 sheet: None (None), residues: 0 loop : -1.20 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 296 TYR 0.016 0.002 TYR B 104 PHE 0.023 0.002 PHE A 240 TRP 0.011 0.001 TRP B 110 HIS 0.003 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (11940) covalent geometry : angle 0.58060 / 0.32 (16284) hydrogen bonds : bond 0.07719 / 5.09 ( 810) hydrogen bonds : angle 4.11144 / 3.02 ( 2403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8560 (t80) REVERT: A 327 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7353 (t80) REVERT: B 81 LYS cc_start: 0.7312 (ttpp) cc_final: 0.6476 (pptt) REVERT: B 327 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7277 (t80) REVERT: B 375 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7506 (mt-10) REVERT: B 392 MET cc_start: 0.7942 (mmt) cc_final: 0.7193 (mmp) REVERT: C 81 LYS cc_start: 0.7426 (ttpp) cc_final: 0.6499 (pptt) REVERT: C 135 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8627 (t80) REVERT: C 375 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7622 (mt-10) REVERT: C 468 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6341 (mmmt) outliers start: 29 outliers final: 15 residues processed: 166 average time/residue: 0.8736 time to fit residues: 163.9363 Evaluate side-chains 150 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 468 LYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 468 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 147 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 ASN C 503 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116489 restraints weight = 34521.427| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.44 r_work: 0.3272 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11940 Z= 0.135 Angle : 0.547 11.063 16284 Z= 0.305 Chirality : 0.067 1.415 1908 Planarity : 0.005 0.048 1947 Dihedral : 4.554 45.661 1591 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.95 % Allowed : 15.98 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.23), residues: 1494 helix: 1.68 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -1.15 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.014 0.001 TYR A 104 PHE 0.022 0.001 PHE C 240 TRP 0.008 0.001 TRP B 110 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (11940) covalent geometry : angle 0.54741 / 0.30 (16284) hydrogen bonds : bond 0.06703 / 4.42 ( 810) hydrogen bonds : angle 4.02870 / 2.96 ( 2403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.7492 (OUTLIER) cc_final: 0.7222 (t) REVERT: A 135 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8653 (t80) REVERT: A 327 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7550 (t80) REVERT: B 81 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6825 (pptt) REVERT: B 135 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: B 327 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7610 (t80) REVERT: B 375 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7784 (mt-10) REVERT: B 392 MET cc_start: 0.8318 (mmt) cc_final: 0.7644 (mmp) REVERT: C 81 LYS cc_start: 0.7550 (ttpp) cc_final: 0.6729 (pptt) REVERT: C 135 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8690 (t80) REVERT: C 311 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7486 (mt-10) outliers start: 24 outliers final: 13 residues processed: 154 average time/residue: 0.9116 time to fit residues: 158.2169 Evaluate side-chains 148 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 468 LYS Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 468 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 ASN B 503 ASN C 503 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110906 restraints weight = 34470.145| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.42 r_work: 0.3197 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11940 Z= 0.177 Angle : 0.605 10.672 16284 Z= 0.338 Chirality : 0.067 1.392 1908 Planarity : 0.006 0.050 1947 Dihedral : 4.518 32.089 1589 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.51 % Allowed : 16.38 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.22), residues: 1494 helix: 1.55 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 296 TYR 0.016 0.002 TYR A 104 PHE 0.026 0.002 PHE A 240 TRP 0.013 0.002 TRP B 110 HIS 0.004 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (11940) covalent geometry : angle 0.60471 / 0.34 (16284) hydrogen bonds : bond 0.08084 / 5.33 ( 810) hydrogen bonds : angle 4.08694 / 3.01 ( 2403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8752 (t80) REVERT: A 327 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7583 (t80) REVERT: B 81 LYS cc_start: 0.7449 (ttpp) cc_final: 0.6794 (pptt) REVERT: B 327 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7686 (t80) REVERT: B 375 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 392 MET cc_start: 0.8370 (mmt) cc_final: 0.7670 (mmp) REVERT: B 426 MET cc_start: 0.8125 (mmm) cc_final: 0.7835 (mmm) REVERT: C 81 LYS cc_start: 0.7548 (ttpp) cc_final: 0.6767 (pptt) REVERT: C 311 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7545 (mt-10) outliers start: 31 outliers final: 21 residues processed: 159 average time/residue: 0.7478 time to fit residues: 134.9580 Evaluate side-chains 156 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 94 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 503 ASN ** C 503 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 = 0.3643 r_free = 0.3643 target = 0.143745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114060 restraints weight = 34589.504| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.47 r_work: 0.3239 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11940 Z= 0.158 Angle : 0.580 10.910 16284 Z= 0.325 Chirality : 0.067 1.412 1908 Planarity : 0.005 0.050 1947 Dihedral : 4.097 15.998 1575 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.95 % Allowed : 16.30 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1494 helix: 1.60 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -1.43 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.015 0.001 TYR C 104 PHE 0.023 0.001 PHE A 240 TRP 0.011 0.001 TRP B 110 HIS 0.004 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (11940) covalent geometry : angle 0.57980 / 0.32 (16284) hydrogen bonds : bond 0.07484 / 4.94 ( 810) hydrogen bonds : angle 4.07387 / 3.00 ( 2403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.7512 (OUTLIER) cc_final: 0.7232 (t) REVERT: A 135 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.8731 (t80) REVERT: A 327 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7598 (t80) REVERT: B 81 LYS cc_start: 0.7485 (ttpp) cc_final: 0.6811 (pptt) REVERT: B 135 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.7067 (m-80) REVERT: B 327 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7673 (t80) REVERT: B 375 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7785 (mt-10) REVERT: B 392 MET cc_start: 0.8354 (mmt) cc_final: 0.7672 (mmp) REVERT: B 426 MET cc_start: 0.8166 (mmm) cc_final: 0.7724 (mmm) REVERT: C 81 LYS cc_start: 0.7552 (ttpp) cc_final: 0.6733 (pptt) REVERT: C 122 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: C 311 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: C 440 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8246 (mt-10) outliers start: 24 outliers final: 12 residues processed: 151 average time/residue: 0.8798 time to fit residues: 150.1650 Evaluate side-chains 150 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 430 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109536 restraints weight = 34532.006| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.48 r_work: 0.3176 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11940 Z= 0.197 Angle : 0.638 10.575 16284 Z= 0.357 Chirality : 0.068 1.394 1908 Planarity : 0.006 0.051 1947 Dihedral : 4.239 17.147 1575 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.51 % Allowed : 16.14 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.22), residues: 1494 helix: 1.45 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.53 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 296 TYR 0.020 0.002 TYR C 135 PHE 0.027 0.002 PHE A 240 TRP 0.014 0.002 TRP B 110 HIS 0.004 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (11940) covalent geometry : angle 0.63794 / 0.36 (16284) hydrogen bonds : bond 0.08729 / 5.75 ( 810) hydrogen bonds : angle 4.15730 / 3.06 ( 2403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.8768 (t80) REVERT: A 327 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7622 (t80) REVERT: B 81 LYS cc_start: 0.7458 (ttpp) cc_final: 0.6809 (pptt) REVERT: B 327 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7718 (t80) REVERT: B 375 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7775 (mt-10) REVERT: B 392 MET cc_start: 0.8436 (mmt) cc_final: 0.7731 (mmp) REVERT: B 426 MET cc_start: 0.8173 (mmm) cc_final: 0.7823 (mmm) REVERT: C 81 LYS cc_start: 0.7547 (ttpp) cc_final: 0.6813 (pptt) REVERT: C 122 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: C 311 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: C 440 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8198 (mt-10) outliers start: 31 outliers final: 19 residues processed: 167 average time/residue: 0.8578 time to fit residues: 163.6636 Evaluate side-chains 157 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 430 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 32 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110953 restraints weight = 34396.081| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.46 r_work: 0.3192 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11940 Z= 0.154 Angle : 0.578 11.026 16284 Z= 0.323 Chirality : 0.067 1.418 1908 Planarity : 0.005 0.051 1947 Dihedral : 4.160 16.502 1575 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.03 % Allowed : 17.19 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.22), residues: 1494 helix: 1.59 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -1.56 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.015 0.001 TYR C 104 PHE 0.022 0.001 PHE C 240 TRP 0.011 0.001 TRP B 110 HIS 0.002 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (11940) covalent geometry : angle 0.57775 / 0.32 (16284) hydrogen bonds : bond 0.07460 / 4.92 ( 810) hydrogen bonds : angle 4.08953 / 3.01 ( 2403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.7538 (OUTLIER) cc_final: 0.7243 (t) REVERT: A 135 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.8730 (t80) REVERT: A 327 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7526 (t80) REVERT: B 81 LYS cc_start: 0.7464 (ttpp) cc_final: 0.6802 (pptt) REVERT: B 135 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: B 327 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7661 (t80) REVERT: B 375 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 392 MET cc_start: 0.8338 (mmt) cc_final: 0.7648 (mmp) REVERT: B 426 MET cc_start: 0.8056 (mmm) cc_final: 0.7738 (mmm) REVERT: C 81 LYS cc_start: 0.7634 (ttpp) cc_final: 0.6872 (pptt) REVERT: C 311 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: C 440 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8178 (mt-10) outliers start: 25 outliers final: 14 residues processed: 152 average time/residue: 0.8974 time to fit residues: 155.0093 Evaluate side-chains 151 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 430 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 60 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 111 optimal weight: 0.0270 chunk 44 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115856 restraints weight = 34384.298| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.41 r_work: 0.3259 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11940 Z= 0.120 Angle : 0.525 11.237 16284 Z= 0.291 Chirality : 0.067 1.419 1908 Planarity : 0.005 0.049 1947 Dihedral : 3.986 16.344 1575 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.70 % Allowed : 17.68 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.23), residues: 1494 helix: 1.87 (0.16), residues: 1173 sheet: None (None), residues: 0 loop : -1.25 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.013 0.001 TYR C 104 PHE 0.020 0.001 PHE B 240 TRP 0.009 0.001 TRP B 110 HIS 0.002 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (11940) covalent geometry : angle 0.52455 / 0.29 (16284) hydrogen bonds : bond 0.05761 / 3.80 ( 810) hydrogen bonds : angle 3.95760 / 2.90 ( 2403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.7167 (t) REVERT: A 135 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8605 (t80) REVERT: A 327 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7374 (t80) REVERT: A 500 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7533 (tp30) REVERT: B 81 LYS cc_start: 0.7466 (ttpp) cc_final: 0.6793 (pptt) REVERT: B 135 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: B 327 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7533 (t80) REVERT: B 375 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7785 (mt-10) REVERT: B 392 MET cc_start: 0.8259 (mmt) cc_final: 0.7398 (mmp) REVERT: C 81 LYS cc_start: 0.7638 (ttpp) cc_final: 0.6846 (pptt) REVERT: C 122 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: C 272 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7568 (mt) REVERT: C 311 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: C 440 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 500 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7548 (tp30) outliers start: 21 outliers final: 9 residues processed: 155 average time/residue: 0.7851 time to fit residues: 138.4327 Evaluate side-chains 151 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 430 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 15 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113090 restraints weight = 34678.479| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.48 r_work: 0.3220 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11940 Z= 0.175 Angle : 0.601 10.672 16284 Z= 0.335 Chirality : 0.067 1.389 1908 Planarity : 0.006 0.050 1947 Dihedral : 4.088 16.524 1575 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.78 % Allowed : 18.25 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.23), residues: 1494 helix: 1.72 (0.15), residues: 1173 sheet: None (None), residues: 0 loop : -1.38 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 296 TYR 0.017 0.002 TYR C 135 PHE 0.026 0.002 PHE A 240 TRP 0.011 0.002 TRP B 110 HIS 0.003 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (11940) covalent geometry : angle 0.60091 / 0.33 (16284) hydrogen bonds : bond 0.07779 / 5.12 ( 810) hydrogen bonds : angle 4.04888 / 2.98 ( 2403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.7528 (OUTLIER) cc_final: 0.7233 (t) REVERT: A 135 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8756 (t80) REVERT: A 327 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7461 (t80) REVERT: B 81 LYS cc_start: 0.7493 (ttpp) cc_final: 0.6818 (pptt) REVERT: B 327 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7729 (t80) REVERT: B 375 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 392 MET cc_start: 0.8361 (mmt) cc_final: 0.7471 (mmp) REVERT: C 81 LYS cc_start: 0.7656 (ttpp) cc_final: 0.6897 (pptt) REVERT: C 122 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: C 311 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7557 (mt-10) outliers start: 22 outliers final: 12 residues processed: 153 average time/residue: 0.8780 time to fit residues: 152.4227 Evaluate side-chains 152 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 47 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113297 restraints weight = 34610.914| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.49 r_work: 0.3229 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 11940 Z= 0.224 Angle : 0.841 59.128 16284 Z= 0.503 Chirality : 0.070 1.392 1908 Planarity : 0.006 0.050 1947 Dihedral : 4.097 16.515 1575 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.62 % Allowed : 18.25 % Favored : 80.13 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1494 helix: 1.71 (0.15), residues: 1173 sheet: None (None), residues: 0 loop : -1.40 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 296 TYR 0.015 0.002 TYR C 135 PHE 0.026 0.002 PHE A 240 TRP 0.011 0.001 TRP B 110 HIS 0.003 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.22 (11940) covalent geometry : angle 0.84147 / 0.50 (16284) hydrogen bonds : bond 0.07649 / 5.04 ( 810) hydrogen bonds : angle 4.05055 / 2.98 ( 2403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6481.72 seconds wall clock time: 110 minutes 19.50 seconds (6619.50 seconds total)