Starting phenix.real_space_refine on Sat Jul 4 18:10:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s88_24890/07_2026/7s88_24890.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s88_24890/07_2026/7s88_24890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s88_24890/07_2026/7s88_24890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s88_24890/07_2026/7s88_24890.map" model { file = "/net/cci-nas-00/data/ceres_data/7s88_24890/07_2026/7s88_24890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s88_24890/07_2026/7s88_24890.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s88_24890/07_2026/7s88_24890.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s88_24890/07_2026/7s88_24890.cif" } resolution = 2.69 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= 0.025 sd= 0.215 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 Ca 1 9.91 5 P 32 5.49 5 S 160 5.16 5 C 14692 2.51 5 N 3392 2.21 5 O 3924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22201 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "B" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "C" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "D" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "A" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 580 Unusual residues: {' CA': 1, 'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 579 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 579 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 579 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 62 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 5.59, per 1000 atoms: 0.25 Number of scatterers: 22201 At special positions: 0 Unit cell: (133.147, 133.147, 122.396, 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) Ca 1 19.99 S 160 16.00 P 32 15.00 O 3924 8.00 N 3392 7.00 C 14692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 940.6 milliseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 66.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 24 through 47 removed outlier: 3.532A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.678A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.541A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.103A pdb=" N GLU A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.540A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.868A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.591A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.569A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.786A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.556A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.072A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 414 through 423 removed outlier: 3.573A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.625A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 5.169A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.140A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 47 removed outlier: 3.531A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.678A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.542A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.104A pdb=" N GLU B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.540A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.868A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.592A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.569A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.787A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.557A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.074A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 414 through 423 removed outlier: 3.572A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.625A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 5.170A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.140A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 47 removed outlier: 3.531A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.678A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.542A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.104A pdb=" N GLU C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.539A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.867A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.592A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.569A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.786A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.556A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.073A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 414 through 423 removed outlier: 3.572A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.625A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 5.170A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.141A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 47 removed outlier: 3.531A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.677A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.542A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.104A pdb=" N GLU D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.539A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.867A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.592A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.568A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.786A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.556A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.073A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 414 through 423 removed outlier: 3.573A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.624A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 5.170A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.140A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.731A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.732A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.731A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.732A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1077 hydrogen bonds defined for protein. 3111 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: 3.35 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3256 1.31 - 1.43: 5696 1.43 - 1.56: 13146 1.56 - 1.69: 122 1.69 - 1.81: 272 Bond restraints: 22492 Sorted by residual: bond pdb=" C21 POV C 702 " pdb=" O21 POV C 702 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C21 POV B 702 " pdb=" O21 POV B 702 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C21 POV A 816 " pdb=" O21 POV A 816 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C21 POV D 706 " pdb=" O21 POV D 706 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV A 808 " pdb=" O21 POV A 808 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 22487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 28746 2.89 - 5.77: 1009 5.77 - 8.66: 235 8.66 - 11.54: 113 11.54 - 14.43: 49 Bond angle restraints: 30152 Sorted by residual: angle pdb=" C ASN B 546 " pdb=" N TYR B 547 " pdb=" CA TYR B 547 " ideal model delta sigma weight residual 121.54 130.82 -9.28 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C ASN D 546 " pdb=" N TYR D 547 " pdb=" CA TYR D 547 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C ASN C 546 " pdb=" N TYR C 547 " pdb=" CA TYR C 547 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ASN A 546 " pdb=" N TYR A 547 " pdb=" CA TYR A 547 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C12 POV D 706 " pdb=" N POV D 706 " pdb=" C14 POV D 706 " ideal model delta sigma weight residual 107.13 121.56 -14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 30147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.74: 12704 30.74 - 61.47: 761 61.47 - 92.20: 103 92.20 - 122.94: 16 122.94 - 153.67: 16 Dihedral angle restraints: 13600 sinusoidal: 6416 harmonic: 7184 Sorted by residual: dihedral pdb=" CA GLU A 68 " pdb=" C GLU A 68 " pdb=" N ASP A 69 " pdb=" CA ASP A 69 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU D 68 " pdb=" C GLU D 68 " pdb=" N ASP D 69 " pdb=" CA ASP D 69 " ideal model delta harmonic sigma weight residual 180.00 152.01 27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLU B 68 " pdb=" C GLU B 68 " pdb=" N ASP B 69 " pdb=" CA ASP B 69 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 13597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2936 0.092 - 0.185: 272 0.185 - 0.277: 11 0.277 - 0.369: 5 0.369 - 0.461: 8 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CG LEU D 458 " pdb=" CB LEU D 458 " pdb=" CD1 LEU D 458 " pdb=" CD2 LEU D 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CG LEU B 458 " pdb=" CB LEU B 458 " pdb=" CD1 LEU B 458 " pdb=" CD2 LEU B 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 3229 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 423 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 424 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 423 " 0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO C 424 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 424 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 424 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 423 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO B 424 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " -0.041 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4472 2.77 - 3.30: 18784 3.30 - 3.83: 36279 3.83 - 4.37: 48614 4.37 - 4.90: 79694 Nonbonded interactions: 187843 Sorted by model distance: nonbonded pdb=" OG1 THR B 242 " pdb=" OE2 GLU B 282 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR D 242 " pdb=" OE2 GLU D 282 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR C 242 " pdb=" OE2 GLU C 282 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR A 242 " pdb=" OE2 GLU A 282 " model vdw 2.235 3.040 nonbonded pdb=" O HOH A 906 " pdb=" O HOH A 916 " model vdw 2.249 3.040 ... (remaining 187838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 637 or resid 806)) selection = (chain 'B' and (resid 24 through 637 or resid 706)) selection = (chain 'C' and (resid 24 through 637 or resid 706)) selection = (chain 'D' and (resid 24 through 637 or resid 706)) } 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=0.45 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.450 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 : 0.013 0.102 22492 Z= 0.571 Angle : 1.479 14.429 30152 Z= 0.649 Chirality : 0.059 0.461 3232 Planarity : 0.009 0.074 3600 Dihedral : 19.322 153.675 8960 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.31 % Allowed : 1.88 % Favored : 96.81 % Cbeta Deviations : 0.17 % 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: -4.89 (0.12), residues: 2448 helix: -3.72 (0.07), residues: 1492 sheet: -1.56 (0.51), residues: 88 loop : -2.08 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 492 TYR 0.023 0.004 TYR D 270 PHE 0.047 0.004 PHE B 472 TRP 0.023 0.004 TRP D 629 HIS 0.014 0.003 HIS C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.01271 / 0.57 (22492) covalent geometry : angle 1.47921 / 0.65 (30152) hydrogen bonds : bond 0.27233 / 18.25 ( 1077) hydrogen bonds : angle 8.31696 / 5.86 ( 3111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 508 time to evaluate : 0.835 Fit side-chains REVERT: A 176 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6245 (mm-30) REVERT: A 234 LEU cc_start: 0.8562 (mp) cc_final: 0.8242 (mm) REVERT: A 239 GLN cc_start: 0.8634 (mt0) cc_final: 0.8332 (mt0) REVERT: A 263 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7669 (mtt90) REVERT: A 442 MET cc_start: 0.8859 (mtt) cc_final: 0.8659 (mtp) REVERT: A 458 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8579 (mt) REVERT: A 635 ASP cc_start: 0.7488 (t70) cc_final: 0.7181 (p0) REVERT: B 176 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6298 (mm-30) REVERT: B 234 LEU cc_start: 0.8593 (mp) cc_final: 0.8288 (mm) REVERT: B 239 GLN cc_start: 0.8649 (mt0) cc_final: 0.8348 (mt0) REVERT: B 263 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7515 (mtt90) REVERT: B 300 LYS cc_start: 0.8143 (mmtp) cc_final: 0.6977 (mppt) REVERT: B 383 ASP cc_start: 0.8071 (m-30) cc_final: 0.7858 (m-30) REVERT: B 635 ASP cc_start: 0.7393 (t70) cc_final: 0.7153 (p0) REVERT: C 176 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6270 (mm-30) REVERT: C 234 LEU cc_start: 0.8593 (mp) cc_final: 0.8290 (mm) REVERT: C 239 GLN cc_start: 0.8649 (mt0) cc_final: 0.8350 (mt0) REVERT: C 263 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7547 (mtt90) REVERT: C 442 MET cc_start: 0.8848 (mtt) cc_final: 0.8644 (mtp) REVERT: C 622 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6854 (pm20) REVERT: C 635 ASP cc_start: 0.7502 (t70) cc_final: 0.7170 (p0) REVERT: D 176 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6267 (mm-30) REVERT: D 234 LEU cc_start: 0.8619 (mp) cc_final: 0.8293 (mm) REVERT: D 239 GLN cc_start: 0.8646 (mt0) cc_final: 0.8349 (mt0) REVERT: D 263 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7647 (mtt90) REVERT: D 300 LYS cc_start: 0.8142 (mmtp) cc_final: 0.6930 (mppt) REVERT: D 442 MET cc_start: 0.8847 (mtt) cc_final: 0.8644 (mtp) REVERT: D 458 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8632 (mt) REVERT: D 635 ASP cc_start: 0.7446 (t70) cc_final: 0.7130 (p0) outliers start: 28 outliers final: 8 residues processed: 532 average time/residue: 0.5979 time to fit residues: 362.2235 Evaluate side-chains 347 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 337 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 122 HIS A 174 ASN A 185 HIS A 214 GLN A 217 ASN A 369 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN A 572 ASN B 37 ASN B 122 HIS B 174 ASN B 185 HIS B 214 GLN B 217 ASN B 306 GLN B 369 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN B 572 ASN C 37 ASN C 118 GLN C 122 HIS C 174 ASN C 185 HIS C 214 GLN C 217 ASN C 369 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 37 ASN D 122 HIS D 174 ASN D 185 HIS D 214 GLN D 217 ASN D 369 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.178716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126964 restraints weight = 21503.709| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.64 r_work: 0.3342 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22492 Z= 0.127 Angle : 0.583 7.667 30152 Z= 0.292 Chirality : 0.039 0.209 3232 Planarity : 0.006 0.055 3600 Dihedral : 21.498 151.708 4212 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.53 % Allowed : 11.16 % Favored : 86.30 % 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: -1.58 (0.16), residues: 2448 helix: -0.77 (0.12), residues: 1524 sheet: -1.09 (0.52), residues: 88 loop : -1.30 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 323 TYR 0.011 0.002 TYR C 555 PHE 0.012 0.001 PHE D 537 TRP 0.014 0.001 TRP B 613 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (22492) covalent geometry : angle 0.58286 / 0.29 (30152) hydrogen bonds : bond 0.04795 / 3.16 ( 1077) hydrogen bonds : angle 3.98827 / 2.80 ( 3111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 373 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7685 (pt0) cc_final: 0.7251 (pm20) REVERT: A 157 CYS cc_start: 0.8308 (m) cc_final: 0.7815 (p) REVERT: A 176 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6021 (mm-30) REVERT: A 177 GLU cc_start: 0.6814 (pm20) cc_final: 0.6601 (pm20) REVERT: A 234 LEU cc_start: 0.8266 (mp) cc_final: 0.8021 (mm) REVERT: A 263 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7374 (mtt90) REVERT: A 279 ASP cc_start: 0.8118 (t0) cc_final: 0.7789 (t0) REVERT: A 314 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7183 (ttmt) REVERT: A 345 MET cc_start: 0.8228 (mtm) cc_final: 0.7774 (mmm) REVERT: A 618 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7977 (mp) REVERT: A 635 ASP cc_start: 0.7814 (t70) cc_final: 0.7228 (p0) REVERT: B 80 GLU cc_start: 0.7726 (pt0) cc_final: 0.7305 (pm20) REVERT: B 146 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7075 (mtp85) REVERT: B 157 CYS cc_start: 0.8275 (m) cc_final: 0.7854 (p) REVERT: B 176 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6127 (mm-30) REVERT: B 234 LEU cc_start: 0.8219 (mp) cc_final: 0.7960 (mm) REVERT: B 263 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7546 (mtt90) REVERT: B 270 TYR cc_start: 0.8233 (t80) cc_final: 0.7928 (t80) REVERT: B 279 ASP cc_start: 0.8119 (t0) cc_final: 0.7803 (t0) REVERT: B 300 LYS cc_start: 0.8011 (mmtp) cc_final: 0.6704 (mppt) REVERT: B 635 ASP cc_start: 0.7839 (t70) cc_final: 0.7240 (p0) REVERT: C 80 GLU cc_start: 0.7684 (pt0) cc_final: 0.7245 (pm20) REVERT: C 157 CYS cc_start: 0.8320 (m) cc_final: 0.7844 (p) REVERT: C 176 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6033 (mm-30) REVERT: C 177 GLU cc_start: 0.6804 (pm20) cc_final: 0.6599 (pm20) REVERT: C 234 LEU cc_start: 0.8253 (mp) cc_final: 0.8011 (mm) REVERT: C 263 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7438 (mtt90) REVERT: C 279 ASP cc_start: 0.8063 (t0) cc_final: 0.7714 (t0) REVERT: C 314 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7326 (ttmt) REVERT: C 345 MET cc_start: 0.8221 (mtm) cc_final: 0.7809 (mmm) REVERT: C 618 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7936 (mp) REVERT: C 635 ASP cc_start: 0.7770 (t70) cc_final: 0.7227 (p0) REVERT: D 80 GLU cc_start: 0.7683 (pt0) cc_final: 0.7249 (pm20) REVERT: D 157 CYS cc_start: 0.8346 (m) cc_final: 0.7865 (p) REVERT: D 176 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6114 (mm-30) REVERT: D 177 GLU cc_start: 0.6830 (pm20) cc_final: 0.6603 (pm20) REVERT: D 234 LEU cc_start: 0.8284 (mp) cc_final: 0.8028 (mm) REVERT: D 263 ARG cc_start: 0.8032 (mtt-85) cc_final: 0.7743 (mtt90) REVERT: D 279 ASP cc_start: 0.8073 (t0) cc_final: 0.7754 (t0) REVERT: D 300 LYS cc_start: 0.7994 (mmtp) cc_final: 0.6647 (mppt) REVERT: D 314 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7180 (ttmt) REVERT: D 345 MET cc_start: 0.8175 (mtm) cc_final: 0.7775 (mmm) REVERT: D 615 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6762 (ttt180) REVERT: D 635 ASP cc_start: 0.7856 (t70) cc_final: 0.7231 (p0) outliers start: 54 outliers final: 12 residues processed: 405 average time/residue: 0.6162 time to fit residues: 285.8539 Evaluate side-chains 365 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 349 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 8 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 203 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 185 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 185 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 185 HIS ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.169186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118936 restraints weight = 21810.315| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.60 r_work: 0.3211 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22492 Z= 0.224 Angle : 0.648 7.261 30152 Z= 0.322 Chirality : 0.043 0.196 3232 Planarity : 0.006 0.055 3600 Dihedral : 20.340 144.664 4208 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.56 % Allowed : 11.21 % Favored : 85.23 % 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: -0.29 (0.17), residues: 2448 helix: 0.42 (0.13), residues: 1504 sheet: -1.15 (0.51), residues: 88 loop : -1.05 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 584 TYR 0.015 0.002 TYR B 555 PHE 0.016 0.002 PHE B 537 TRP 0.019 0.002 TRP B 613 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.22 (22492) covalent geometry : angle 0.64845 / 0.32 (30152) hydrogen bonds : bond 0.05345 / 3.53 ( 1077) hydrogen bonds : angle 3.85665 / 2.70 ( 3111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 346 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7595 (pt0) cc_final: 0.7251 (pm20) REVERT: A 104 GLU cc_start: 0.6696 (pm20) cc_final: 0.6480 (pm20) REVERT: A 176 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6121 (mm-30) REVERT: A 234 LEU cc_start: 0.8165 (mp) cc_final: 0.7753 (mm) REVERT: A 263 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.7628 (mtt90) REVERT: A 279 ASP cc_start: 0.8268 (t0) cc_final: 0.7958 (t0) REVERT: A 589 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7215 (ttp80) REVERT: A 614 PRO cc_start: 0.9076 (Cg_exo) cc_final: 0.8818 (Cg_endo) REVERT: A 618 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7885 (mp) REVERT: A 635 ASP cc_start: 0.7726 (t70) cc_final: 0.7043 (p0) REVERT: B 31 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6528 (tt0) REVERT: B 80 GLU cc_start: 0.7569 (pt0) cc_final: 0.7236 (pm20) REVERT: B 176 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6061 (mm-30) REVERT: B 177 GLU cc_start: 0.6876 (pm20) cc_final: 0.6667 (pm20) REVERT: B 234 LEU cc_start: 0.8235 (mp) cc_final: 0.7772 (mm) REVERT: B 263 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7503 (mtt90) REVERT: B 279 ASP cc_start: 0.8318 (t0) cc_final: 0.8016 (t0) REVERT: B 323 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7851 (mpt-90) REVERT: B 357 ASN cc_start: 0.7999 (p0) cc_final: 0.7789 (p0) REVERT: B 589 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7215 (ttp80) REVERT: B 618 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7988 (mp) REVERT: B 628 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7693 (mtp180) REVERT: B 635 ASP cc_start: 0.7718 (t70) cc_final: 0.7028 (p0) REVERT: C 80 GLU cc_start: 0.7605 (pt0) cc_final: 0.7258 (pm20) REVERT: C 176 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6073 (mm-30) REVERT: C 234 LEU cc_start: 0.8191 (mp) cc_final: 0.7792 (mm) REVERT: C 263 ARG cc_start: 0.8217 (mtt-85) cc_final: 0.7732 (mtt90) REVERT: C 279 ASP cc_start: 0.8277 (t0) cc_final: 0.7916 (t0) REVERT: C 314 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7295 (ttmt) REVERT: C 589 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7195 (ttp80) REVERT: C 618 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7907 (mp) REVERT: C 628 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7675 (mtp180) REVERT: C 635 ASP cc_start: 0.7758 (t70) cc_final: 0.7066 (p0) REVERT: D 80 GLU cc_start: 0.7608 (pt0) cc_final: 0.7258 (pm20) REVERT: D 104 GLU cc_start: 0.6663 (pm20) cc_final: 0.6450 (pm20) REVERT: D 176 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6071 (mm-30) REVERT: D 234 LEU cc_start: 0.8221 (mp) cc_final: 0.7765 (mm) REVERT: D 263 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7677 (mtt90) REVERT: D 279 ASP cc_start: 0.8276 (t0) cc_final: 0.7964 (t0) REVERT: D 589 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7223 (ttp80) REVERT: D 615 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6855 (ttt180) REVERT: D 618 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7973 (mp) REVERT: D 628 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7723 (mtp180) REVERT: D 635 ASP cc_start: 0.7681 (t70) cc_final: 0.6988 (p0) outliers start: 76 outliers final: 25 residues processed: 386 average time/residue: 0.6287 time to fit residues: 277.1195 Evaluate side-chains 364 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 325 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 589 ARG Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 615 ARG Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 628 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 GLN B 185 HIS ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 369 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.173214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125147 restraints weight = 21769.934| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.54 r_work: 0.3306 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22492 Z= 0.139 Angle : 0.542 6.415 30152 Z= 0.274 Chirality : 0.039 0.180 3232 Planarity : 0.005 0.050 3600 Dihedral : 19.253 139.056 4208 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.19 % Allowed : 12.71 % Favored : 84.10 % 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: 0.50 (0.17), residues: 2448 helix: 1.11 (0.13), residues: 1500 sheet: -1.17 (0.50), residues: 88 loop : -0.80 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 33 TYR 0.012 0.002 TYR D 555 PHE 0.012 0.001 PHE A 537 TRP 0.011 0.001 TRP B 613 HIS 0.002 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (22492) covalent geometry : angle 0.54185 / 0.27 (30152) hydrogen bonds : bond 0.04329 / 2.86 ( 1077) hydrogen bonds : angle 3.64307 / 2.55 ( 3111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 330 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7031 (mtp85) REVERT: A 157 CYS cc_start: 0.8235 (m) cc_final: 0.7815 (p) REVERT: A 176 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6162 (mm-30) REVERT: A 234 LEU cc_start: 0.8266 (mp) cc_final: 0.7943 (mm) REVERT: A 263 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7714 (mtt90) REVERT: A 279 ASP cc_start: 0.8342 (t0) cc_final: 0.8022 (t0) REVERT: A 314 LYS cc_start: 0.7983 (ttpt) cc_final: 0.7279 (ttmt) REVERT: A 614 PRO cc_start: 0.9079 (Cg_exo) cc_final: 0.8871 (Cg_endo) REVERT: A 618 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7998 (mp) REVERT: A 635 ASP cc_start: 0.7584 (t70) cc_final: 0.7020 (p0) REVERT: B 80 GLU cc_start: 0.7514 (pt0) cc_final: 0.7307 (pm20) REVERT: B 146 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7007 (mtp85) REVERT: B 157 CYS cc_start: 0.8248 (m) cc_final: 0.7839 (p) REVERT: B 176 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6186 (mm-30) REVERT: B 234 LEU cc_start: 0.8304 (mp) cc_final: 0.7944 (mm) REVERT: B 263 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7682 (mtt90) REVERT: B 279 ASP cc_start: 0.8378 (t0) cc_final: 0.8053 (t0) REVERT: B 314 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7247 (ttmt) REVERT: B 323 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7914 (mpt-90) REVERT: B 357 ASN cc_start: 0.8059 (p0) cc_final: 0.7845 (p0) REVERT: B 610 ARG cc_start: 0.7665 (tpp-160) cc_final: 0.7451 (tpp-160) REVERT: B 618 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 628 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7745 (mtp180) REVERT: B 635 ASP cc_start: 0.7593 (t70) cc_final: 0.7010 (p0) REVERT: C 146 ARG cc_start: 0.7708 (mtm110) cc_final: 0.7009 (mtp85) REVERT: C 157 CYS cc_start: 0.8299 (m) cc_final: 0.7866 (p) REVERT: C 176 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6073 (mm-30) REVERT: C 234 LEU cc_start: 0.8252 (mp) cc_final: 0.7930 (mm) REVERT: C 263 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.7839 (mtt90) REVERT: C 279 ASP cc_start: 0.8403 (t0) cc_final: 0.8067 (t0) REVERT: C 314 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7415 (ttmt) REVERT: C 345 MET cc_start: 0.8193 (mtm) cc_final: 0.7799 (mmm) REVERT: C 610 ARG cc_start: 0.7758 (tpp-160) cc_final: 0.7542 (tpp-160) REVERT: C 618 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8012 (mp) REVERT: C 628 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7726 (mtp180) REVERT: C 635 ASP cc_start: 0.7622 (t70) cc_final: 0.7045 (p0) REVERT: D 146 ARG cc_start: 0.7721 (mtm110) cc_final: 0.7015 (mtp85) REVERT: D 157 CYS cc_start: 0.8257 (m) cc_final: 0.7827 (p) REVERT: D 176 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6164 (mm-30) REVERT: D 234 LEU cc_start: 0.8270 (mp) cc_final: 0.7919 (mm) REVERT: D 263 ARG cc_start: 0.8223 (mtt-85) cc_final: 0.7754 (mtt90) REVERT: D 279 ASP cc_start: 0.8315 (t0) cc_final: 0.8003 (t0) REVERT: D 314 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7280 (ttmt) REVERT: D 610 ARG cc_start: 0.7727 (tpp-160) cc_final: 0.7524 (tpp-160) REVERT: D 628 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7722 (mtp180) REVERT: D 635 ASP cc_start: 0.7595 (t70) cc_final: 0.7016 (p0) outliers start: 68 outliers final: 26 residues processed: 363 average time/residue: 0.6058 time to fit residues: 250.6979 Evaluate side-chains 353 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 318 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 628 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 12 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 236 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS B 185 HIS B 369 GLN C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124399 restraints weight = 21779.931| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.55 r_work: 0.3295 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22492 Z= 0.149 Angle : 0.553 6.476 30152 Z= 0.278 Chirality : 0.039 0.187 3232 Planarity : 0.005 0.049 3600 Dihedral : 18.477 128.562 4208 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.67 % Allowed : 13.46 % Favored : 83.86 % 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: 0.84 (0.17), residues: 2448 helix: 1.38 (0.14), residues: 1500 sheet: -1.09 (0.49), residues: 88 loop : -0.66 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.013 0.002 TYR B 555 PHE 0.012 0.001 PHE D 537 TRP 0.010 0.001 TRP A 495 HIS 0.003 0.001 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (22492) covalent geometry : angle 0.55267 / 0.28 (30152) hydrogen bonds : bond 0.04403 / 2.91 ( 1077) hydrogen bonds : angle 3.58200 / 2.51 ( 3111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 320 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.8263 (m) cc_final: 0.7829 (p) REVERT: A 176 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6113 (mm-30) REVERT: A 234 LEU cc_start: 0.8234 (mp) cc_final: 0.7878 (mm) REVERT: A 263 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7738 (mtt90) REVERT: A 279 ASP cc_start: 0.8416 (t0) cc_final: 0.8100 (t0) REVERT: A 314 LYS cc_start: 0.7974 (ttpt) cc_final: 0.7281 (ttmt) REVERT: A 618 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8026 (mp) REVERT: B 157 CYS cc_start: 0.8259 (m) cc_final: 0.7860 (p) REVERT: B 176 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6115 (mm-30) REVERT: B 234 LEU cc_start: 0.8249 (mp) cc_final: 0.7845 (mm) REVERT: B 263 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7711 (mtt90) REVERT: B 279 ASP cc_start: 0.8437 (t0) cc_final: 0.8120 (t0) REVERT: B 314 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7269 (ttmt) REVERT: B 323 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7922 (mpt-90) REVERT: B 357 ASN cc_start: 0.8054 (p0) cc_final: 0.7851 (p0) REVERT: B 610 ARG cc_start: 0.7659 (tpp-160) cc_final: 0.7447 (tpp-160) REVERT: B 618 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 628 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7759 (mtp180) REVERT: C 146 ARG cc_start: 0.7663 (mtm110) cc_final: 0.6968 (mtp85) REVERT: C 157 CYS cc_start: 0.8293 (m) cc_final: 0.7861 (p) REVERT: C 176 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6153 (mm-30) REVERT: C 234 LEU cc_start: 0.8224 (mp) cc_final: 0.7887 (mm) REVERT: C 263 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.7855 (mtt90) REVERT: C 314 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7366 (ttmt) REVERT: C 610 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7487 (tpp-160) REVERT: C 614 PRO cc_start: 0.9093 (Cg_exo) cc_final: 0.8877 (Cg_endo) REVERT: C 618 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8035 (mp) REVERT: C 628 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7780 (mtp180) REVERT: D 157 CYS cc_start: 0.8275 (m) cc_final: 0.7836 (p) REVERT: D 176 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6128 (mm-30) REVERT: D 214 GLN cc_start: 0.7660 (mt0) cc_final: 0.7434 (mt0) REVERT: D 234 LEU cc_start: 0.8235 (mp) cc_final: 0.7856 (mm) REVERT: D 263 ARG cc_start: 0.8195 (mtt-85) cc_final: 0.7766 (mtt90) REVERT: D 279 ASP cc_start: 0.8425 (t0) cc_final: 0.8101 (t0) REVERT: D 290 GLN cc_start: 0.8433 (mt0) cc_final: 0.8228 (mt0) REVERT: D 314 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7245 (ttmt) REVERT: D 610 ARG cc_start: 0.7688 (tpp-160) cc_final: 0.7463 (tpp-160) REVERT: D 618 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8121 (mp) REVERT: D 628 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7759 (mtp180) outliers start: 57 outliers final: 35 residues processed: 341 average time/residue: 0.6261 time to fit residues: 244.3705 Evaluate side-chains 360 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 316 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 628 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 181 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 189 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 185 HIS B 118 GLN B 185 HIS C 118 GLN C 185 HIS C 369 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 118 GLN D 185 HIS D 369 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.176229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128627 restraints weight = 21931.737| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.59 r_work: 0.3348 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22492 Z= 0.103 Angle : 0.491 6.262 30152 Z= 0.247 Chirality : 0.037 0.178 3232 Planarity : 0.005 0.047 3600 Dihedral : 17.321 114.437 4208 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.53 % Allowed : 13.88 % Favored : 83.58 % 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: 1.17 (0.18), residues: 2448 helix: 1.65 (0.14), residues: 1508 sheet: -0.96 (0.51), residues: 88 loop : -0.57 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 323 TYR 0.011 0.001 TYR A 524 PHE 0.009 0.001 PHE A 537 TRP 0.010 0.001 TRP A 495 HIS 0.002 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (22492) covalent geometry : angle 0.49062 / 0.25 (30152) hydrogen bonds : bond 0.03712 / 2.45 ( 1077) hydrogen bonds : angle 3.43102 / 2.40 ( 3111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 308 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7577 (mtm110) cc_final: 0.6930 (mtp85) REVERT: A 157 CYS cc_start: 0.8217 (m) cc_final: 0.7915 (p) REVERT: A 176 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6167 (mm-30) REVERT: A 234 LEU cc_start: 0.8142 (mp) cc_final: 0.7877 (mm) REVERT: A 263 ARG cc_start: 0.8172 (mtt-85) cc_final: 0.7712 (mtt90) REVERT: A 279 ASP cc_start: 0.8363 (t0) cc_final: 0.8036 (t0) REVERT: A 314 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7359 (ttmt) REVERT: A 345 MET cc_start: 0.8134 (mtm) cc_final: 0.7777 (mmm) REVERT: A 635 ASP cc_start: 0.7592 (t70) cc_final: 0.6980 (p0) REVERT: B 146 ARG cc_start: 0.7563 (mtm110) cc_final: 0.6908 (mtp85) REVERT: B 157 CYS cc_start: 0.8217 (m) cc_final: 0.7994 (p) REVERT: B 176 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6250 (mm-30) REVERT: B 177 GLU cc_start: 0.6915 (pm20) cc_final: 0.6149 (pt0) REVERT: B 234 LEU cc_start: 0.8205 (mp) cc_final: 0.7880 (mm) REVERT: B 263 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7886 (mtt90) REVERT: B 279 ASP cc_start: 0.8379 (t0) cc_final: 0.8040 (t0) REVERT: B 300 LYS cc_start: 0.8065 (mttm) cc_final: 0.6876 (mppt) REVERT: B 314 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7305 (ttmt) REVERT: B 323 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7957 (mpt-90) REVERT: B 628 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7734 (mtp180) REVERT: B 635 ASP cc_start: 0.7608 (t70) cc_final: 0.7042 (p0) REVERT: C 146 ARG cc_start: 0.7588 (mtm110) cc_final: 0.6948 (mtp85) REVERT: C 157 CYS cc_start: 0.8240 (m) cc_final: 0.7939 (p) REVERT: C 176 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6127 (mm-30) REVERT: C 177 GLU cc_start: 0.6900 (pm20) cc_final: 0.6149 (pt0) REVERT: C 234 LEU cc_start: 0.8146 (mp) cc_final: 0.7852 (mm) REVERT: C 263 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7865 (mtt90) REVERT: C 314 LYS cc_start: 0.7905 (ttpt) cc_final: 0.7368 (ttmt) REVERT: C 345 MET cc_start: 0.8133 (mtm) cc_final: 0.7783 (mmm) REVERT: C 610 ARG cc_start: 0.7662 (tpp-160) cc_final: 0.7384 (tpp-160) REVERT: C 628 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7744 (mtp180) REVERT: C 635 ASP cc_start: 0.7591 (t70) cc_final: 0.7050 (p0) REVERT: D 146 ARG cc_start: 0.7557 (mtm110) cc_final: 0.6911 (mtp85) REVERT: D 157 CYS cc_start: 0.8271 (m) cc_final: 0.7964 (p) REVERT: D 176 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6244 (mm-30) REVERT: D 177 GLU cc_start: 0.6866 (pm20) cc_final: 0.6099 (pt0) REVERT: D 234 LEU cc_start: 0.8226 (mp) cc_final: 0.7905 (mm) REVERT: D 263 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7895 (mtt90) REVERT: D 279 ASP cc_start: 0.8417 (t0) cc_final: 0.8088 (t0) REVERT: D 314 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7329 (ttmt) REVERT: D 345 MET cc_start: 0.8136 (mtm) cc_final: 0.7787 (mmm) REVERT: D 610 ARG cc_start: 0.7697 (tpp-160) cc_final: 0.7415 (tpp-160) REVERT: D 628 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7736 (mtp180) REVERT: D 635 ASP cc_start: 0.7591 (t70) cc_final: 0.7032 (p0) outliers start: 54 outliers final: 24 residues processed: 336 average time/residue: 0.6377 time to fit residues: 245.2398 Evaluate side-chains 329 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 299 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 628 ARG Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 628 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 165 optimal weight: 0.6980 chunk 224 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS A 369 GLN B 185 HIS C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.177267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.132821 restraints weight = 21916.279| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.57 r_work: 0.3357 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22492 Z= 0.102 Angle : 0.490 6.414 30152 Z= 0.247 Chirality : 0.037 0.174 3232 Planarity : 0.004 0.048 3600 Dihedral : 16.575 98.124 4208 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.58 % Allowed : 14.26 % Favored : 83.16 % 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: 1.38 (0.18), residues: 2448 helix: 1.80 (0.14), residues: 1508 sheet: -0.78 (0.53), residues: 88 loop : -0.46 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 323 TYR 0.011 0.001 TYR D 524 PHE 0.010 0.001 PHE A 537 TRP 0.013 0.001 TRP A 583 HIS 0.002 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (22492) covalent geometry : angle 0.48991 / 0.25 (30152) hydrogen bonds : bond 0.03683 / 2.43 ( 1077) hydrogen bonds : angle 3.38094 / 2.37 ( 3111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 314 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7542 (mtm110) cc_final: 0.6902 (mtp85) REVERT: A 157 CYS cc_start: 0.8202 (m) cc_final: 0.7990 (p) REVERT: A 176 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6145 (mm-30) REVERT: A 177 GLU cc_start: 0.6858 (pm20) cc_final: 0.6168 (pt0) REVERT: A 234 LEU cc_start: 0.8087 (mp) cc_final: 0.7785 (mm) REVERT: A 263 ARG cc_start: 0.8126 (mtt-85) cc_final: 0.7656 (mtt90) REVERT: A 314 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7315 (ttmt) REVERT: A 345 MET cc_start: 0.8121 (mtm) cc_final: 0.7758 (mmm) REVERT: A 578 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8558 (mtm) REVERT: A 635 ASP cc_start: 0.7575 (t70) cc_final: 0.7013 (p0) REVERT: B 146 ARG cc_start: 0.7558 (mtm110) cc_final: 0.6918 (mtp85) REVERT: B 157 CYS cc_start: 0.8225 (m) cc_final: 0.7997 (p) REVERT: B 176 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6233 (mm-30) REVERT: B 177 GLU cc_start: 0.6891 (pm20) cc_final: 0.6667 (pm20) REVERT: B 234 LEU cc_start: 0.8190 (mp) cc_final: 0.7848 (mm) REVERT: B 263 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7813 (mtt90) REVERT: B 279 ASP cc_start: 0.8437 (t0) cc_final: 0.8114 (t0) REVERT: B 300 LYS cc_start: 0.8080 (mttm) cc_final: 0.6838 (mppt) REVERT: B 314 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7290 (ttmt) REVERT: B 578 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8565 (mtm) REVERT: B 635 ASP cc_start: 0.7586 (t70) cc_final: 0.7021 (p0) REVERT: C 146 ARG cc_start: 0.7559 (mtm110) cc_final: 0.6923 (mtp85) REVERT: C 157 CYS cc_start: 0.8227 (m) cc_final: 0.8011 (p) REVERT: C 176 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6222 (mm-30) REVERT: C 177 GLU cc_start: 0.6879 (pm20) cc_final: 0.6655 (pm20) REVERT: C 234 LEU cc_start: 0.8127 (mp) cc_final: 0.7832 (mm) REVERT: C 263 ARG cc_start: 0.8179 (mtt-85) cc_final: 0.7972 (mtt90) REVERT: C 314 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7321 (ttmt) REVERT: C 345 MET cc_start: 0.8119 (mtm) cc_final: 0.7756 (mmm) REVERT: C 610 ARG cc_start: 0.7647 (tpp-160) cc_final: 0.7392 (tpp-160) REVERT: C 618 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 635 ASP cc_start: 0.7590 (t70) cc_final: 0.7031 (p0) REVERT: D 146 ARG cc_start: 0.7528 (mtm110) cc_final: 0.6884 (mtp85) REVERT: D 157 CYS cc_start: 0.8257 (m) cc_final: 0.7954 (p) REVERT: D 176 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6220 (mm-30) REVERT: D 177 GLU cc_start: 0.6868 (pm20) cc_final: 0.6656 (pm20) REVERT: D 234 LEU cc_start: 0.8186 (mp) cc_final: 0.7840 (mm) REVERT: D 263 ARG cc_start: 0.8120 (mtt-85) cc_final: 0.7844 (mtt90) REVERT: D 314 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7284 (ttmt) REVERT: D 345 MET cc_start: 0.8119 (mtm) cc_final: 0.7762 (mmm) REVERT: D 578 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8553 (mtm) REVERT: D 610 ARG cc_start: 0.7678 (tpp-160) cc_final: 0.7429 (tpp-160) REVERT: D 635 ASP cc_start: 0.7587 (t70) cc_final: 0.7022 (p0) outliers start: 55 outliers final: 26 residues processed: 340 average time/residue: 0.6225 time to fit residues: 243.0230 Evaluate side-chains 330 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 578 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 40 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 13 optimal weight: 0.0030 chunk 86 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS A 546 ASN B 185 HIS ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.176455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128762 restraints weight = 21789.814| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.61 r_work: 0.3338 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22492 Z= 0.106 Angle : 0.497 6.452 30152 Z= 0.249 Chirality : 0.038 0.178 3232 Planarity : 0.004 0.046 3600 Dihedral : 16.109 88.715 4208 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.02 % Allowed : 14.87 % Favored : 83.11 % 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: 1.45 (0.18), residues: 2448 helix: 1.83 (0.14), residues: 1508 sheet: -0.74 (0.54), residues: 88 loop : -0.38 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 323 TYR 0.010 0.001 TYR A 555 PHE 0.009 0.001 PHE B 537 TRP 0.016 0.001 TRP C 583 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (22492) covalent geometry : angle 0.49665 / 0.25 (30152) hydrogen bonds : bond 0.03751 / 2.47 ( 1077) hydrogen bonds : angle 3.38181 / 2.36 ( 3111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7794 (t0) cc_final: 0.7486 (t160) REVERT: A 146 ARG cc_start: 0.7543 (mtm110) cc_final: 0.6890 (mtp85) REVERT: A 157 CYS cc_start: 0.8204 (m) cc_final: 0.7990 (p) REVERT: A 176 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6139 (mm-30) REVERT: A 233 ASP cc_start: 0.7547 (p0) cc_final: 0.7273 (p0) REVERT: A 234 LEU cc_start: 0.8027 (mp) cc_final: 0.7769 (mm) REVERT: A 263 ARG cc_start: 0.8134 (mtt-85) cc_final: 0.7671 (mtt90) REVERT: A 314 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7350 (ttmt) REVERT: A 345 MET cc_start: 0.8130 (mtm) cc_final: 0.7781 (mmm) REVERT: A 635 ASP cc_start: 0.7603 (t70) cc_final: 0.7017 (p0) REVERT: B 146 ARG cc_start: 0.7500 (mtm110) cc_final: 0.6846 (mtp85) REVERT: B 157 CYS cc_start: 0.8221 (m) cc_final: 0.7991 (p) REVERT: B 176 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6160 (mm-30) REVERT: B 234 LEU cc_start: 0.8166 (mp) cc_final: 0.7816 (mm) REVERT: B 263 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7834 (mtt90) REVERT: B 279 ASP cc_start: 0.8434 (t0) cc_final: 0.8220 (t0) REVERT: B 300 LYS cc_start: 0.8082 (mttm) cc_final: 0.6827 (mppt) REVERT: B 314 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7287 (ttmt) REVERT: B 323 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7978 (mpt-90) REVERT: B 635 ASP cc_start: 0.7591 (t70) cc_final: 0.7017 (p0) REVERT: C 146 ARG cc_start: 0.7516 (mtm110) cc_final: 0.6867 (mtp85) REVERT: C 157 CYS cc_start: 0.8231 (m) cc_final: 0.8009 (p) REVERT: C 176 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6517 (mp0) REVERT: C 234 LEU cc_start: 0.8106 (mp) cc_final: 0.7788 (mm) REVERT: C 314 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7340 (ttmt) REVERT: C 345 MET cc_start: 0.8140 (mtm) cc_final: 0.7790 (mmm) REVERT: C 610 ARG cc_start: 0.7583 (tpp-160) cc_final: 0.7365 (tpp-160) REVERT: C 635 ASP cc_start: 0.7603 (t70) cc_final: 0.7016 (p0) REVERT: D 146 ARG cc_start: 0.7522 (mtm110) cc_final: 0.6867 (mtp85) REVERT: D 157 CYS cc_start: 0.8286 (m) cc_final: 0.8043 (p) REVERT: D 176 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6181 (mm-30) REVERT: D 177 GLU cc_start: 0.6925 (pm20) cc_final: 0.6679 (pm20) REVERT: D 234 LEU cc_start: 0.8168 (mp) cc_final: 0.7834 (mm) REVERT: D 263 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7809 (mtt90) REVERT: D 314 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7320 (ttmt) REVERT: D 345 MET cc_start: 0.8125 (mtm) cc_final: 0.7780 (mmm) REVERT: D 610 ARG cc_start: 0.7615 (tpp-160) cc_final: 0.7408 (tpp-160) REVERT: D 618 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8156 (mp) REVERT: D 635 ASP cc_start: 0.7584 (t70) cc_final: 0.7012 (p0) outliers start: 43 outliers final: 28 residues processed: 326 average time/residue: 0.6177 time to fit residues: 231.5004 Evaluate side-chains 325 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 218 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 185 HIS B 118 GLN B 174 ASN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 185 HIS D 369 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.172197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123518 restraints weight = 21814.615| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.56 r_work: 0.3282 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22492 Z= 0.185 Angle : 0.587 7.029 30152 Z= 0.292 Chirality : 0.042 0.199 3232 Planarity : 0.005 0.049 3600 Dihedral : 16.418 96.005 4208 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.02 % Allowed : 14.82 % Favored : 83.16 % 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: 1.22 (0.17), residues: 2448 helix: 1.63 (0.13), residues: 1500 sheet: -0.85 (0.50), residues: 88 loop : -0.42 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 263 TYR 0.014 0.002 TYR C 555 PHE 0.012 0.001 PHE A 512 TRP 0.017 0.002 TRP A 583 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.18 (22492) covalent geometry : angle 0.58715 / 0.29 (30152) hydrogen bonds : bond 0.04627 / 3.06 ( 1077) hydrogen bonds : angle 3.55754 / 2.49 ( 3111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.8219 (m) cc_final: 0.7805 (p) REVERT: A 176 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6148 (mm-30) REVERT: A 234 LEU cc_start: 0.8218 (mp) cc_final: 0.7867 (mm) REVERT: A 263 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7741 (mtt90) REVERT: A 314 LYS cc_start: 0.8032 (ttpt) cc_final: 0.7306 (ttmt) REVERT: A 618 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8074 (mp) REVERT: B 157 CYS cc_start: 0.8260 (m) cc_final: 0.7825 (p) REVERT: B 176 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6169 (mm-30) REVERT: B 177 GLU cc_start: 0.6807 (pm20) cc_final: 0.6063 (pt0) REVERT: B 234 LEU cc_start: 0.8248 (mp) cc_final: 0.7834 (mm) REVERT: B 263 ARG cc_start: 0.8214 (mtt-85) cc_final: 0.7956 (mtt90) REVERT: B 314 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7260 (ttmt) REVERT: B 323 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7908 (mpt-90) REVERT: B 610 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.7510 (tpp-160) REVERT: C 157 CYS cc_start: 0.8263 (m) cc_final: 0.7840 (p) REVERT: C 176 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6532 (mp0) REVERT: C 177 GLU cc_start: 0.6828 (pm20) cc_final: 0.6110 (pt0) REVERT: C 214 GLN cc_start: 0.7664 (mt0) cc_final: 0.7444 (mt0) REVERT: C 234 LEU cc_start: 0.8220 (mp) cc_final: 0.7837 (mm) REVERT: C 314 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7341 (ttmt) REVERT: C 610 ARG cc_start: 0.7722 (tpp-160) cc_final: 0.7522 (tpp-160) REVERT: D 157 CYS cc_start: 0.8264 (m) cc_final: 0.7813 (p) REVERT: D 176 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6196 (mm-30) REVERT: D 177 GLU cc_start: 0.7010 (pm20) cc_final: 0.6725 (pm20) REVERT: D 234 LEU cc_start: 0.8253 (mp) cc_final: 0.7866 (mm) REVERT: D 263 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7941 (mtt90) REVERT: D 314 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7287 (ttmt) REVERT: D 610 ARG cc_start: 0.7725 (tpp-160) cc_final: 0.7469 (tpp-160) REVERT: D 618 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8136 (mp) outliers start: 43 outliers final: 24 residues processed: 328 average time/residue: 0.6441 time to fit residues: 241.6452 Evaluate side-chains 322 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 295 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 90 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 203 optimal weight: 0.0020 chunk 38 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS A 369 GLN B 174 ASN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.175268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127553 restraints weight = 21864.837| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.58 r_work: 0.3328 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22492 Z= 0.114 Angle : 0.513 7.566 30152 Z= 0.257 Chirality : 0.038 0.184 3232 Planarity : 0.004 0.046 3600 Dihedral : 15.848 85.972 4208 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.78 % Allowed : 15.10 % Favored : 83.11 % 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: 1.40 (0.17), residues: 2448 helix: 1.79 (0.14), residues: 1508 sheet: -0.82 (0.51), residues: 88 loop : -0.40 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 323 TYR 0.011 0.001 TYR D 555 PHE 0.009 0.001 PHE D 537 TRP 0.017 0.001 TRP D 583 HIS 0.004 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (22492) covalent geometry : angle 0.51274 / 0.26 (30152) hydrogen bonds : bond 0.03879 / 2.56 ( 1077) hydrogen bonds : angle 3.42639 / 2.40 ( 3111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7573 (mtm110) cc_final: 0.6931 (mtp85) REVERT: A 157 CYS cc_start: 0.8184 (m) cc_final: 0.7946 (p) REVERT: A 176 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6084 (mm-30) REVERT: A 177 GLU cc_start: 0.6784 (pm20) cc_final: 0.6138 (pt0) REVERT: A 233 ASP cc_start: 0.7605 (p0) cc_final: 0.7384 (p0) REVERT: A 234 LEU cc_start: 0.8102 (mp) cc_final: 0.7814 (mm) REVERT: A 263 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7614 (mtt90) REVERT: A 314 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7201 (ttmt) REVERT: B 146 ARG cc_start: 0.7522 (mtm110) cc_final: 0.6848 (mtp85) REVERT: B 157 CYS cc_start: 0.8181 (m) cc_final: 0.7946 (p) REVERT: B 176 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6174 (mm-30) REVERT: B 177 GLU cc_start: 0.6813 (pm20) cc_final: 0.6054 (pt0) REVERT: B 234 LEU cc_start: 0.8212 (mp) cc_final: 0.7853 (mm) REVERT: B 263 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7905 (mtt90) REVERT: B 279 ASP cc_start: 0.8419 (t0) cc_final: 0.8193 (t0) REVERT: B 314 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7220 (ttmt) REVERT: B 323 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7904 (mpt-90) REVERT: B 618 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8103 (mp) REVERT: C 129 ASN cc_start: 0.7683 (t0) cc_final: 0.7372 (t160) REVERT: C 146 ARG cc_start: 0.7517 (mtm110) cc_final: 0.6885 (mtp85) REVERT: C 157 CYS cc_start: 0.8204 (m) cc_final: 0.7962 (p) REVERT: C 176 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6534 (mp0) REVERT: C 177 GLU cc_start: 0.6836 (pm20) cc_final: 0.6104 (pt0) REVERT: C 233 ASP cc_start: 0.7796 (p0) cc_final: 0.7558 (p0) REVERT: C 234 LEU cc_start: 0.8105 (mp) cc_final: 0.7796 (mm) REVERT: C 314 LYS cc_start: 0.7850 (ttpt) cc_final: 0.7238 (ttmt) REVERT: C 635 ASP cc_start: 0.7601 (t70) cc_final: 0.7004 (p0) REVERT: D 146 ARG cc_start: 0.7555 (mtm110) cc_final: 0.6915 (mtp85) REVERT: D 157 CYS cc_start: 0.8201 (m) cc_final: 0.7889 (p) REVERT: D 176 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6168 (mm-30) REVERT: D 177 GLU cc_start: 0.6886 (pm20) cc_final: 0.6617 (pm20) REVERT: D 234 LEU cc_start: 0.8212 (mp) cc_final: 0.7861 (mm) REVERT: D 263 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7826 (mtt90) REVERT: D 314 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7235 (ttmt) REVERT: D 610 ARG cc_start: 0.7620 (tpp-160) cc_final: 0.7395 (tpp-160) REVERT: D 618 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8132 (mp) REVERT: D 635 ASP cc_start: 0.7592 (t70) cc_final: 0.6992 (p0) outliers start: 38 outliers final: 23 residues processed: 324 average time/residue: 0.6422 time to fit residues: 238.0318 Evaluate side-chains 324 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 298 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 122 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS A 214 GLN B 357 ASN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 369 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126582 restraints weight = 21693.231| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.58 r_work: 0.3317 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22492 Z= 0.137 Angle : 0.543 7.656 30152 Z= 0.272 Chirality : 0.039 0.183 3232 Planarity : 0.005 0.046 3600 Dihedral : 15.783 86.474 4208 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.83 % Allowed : 15.06 % Favored : 83.11 % 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: 1.39 (0.17), residues: 2448 helix: 1.79 (0.14), residues: 1500 sheet: -0.86 (0.51), residues: 88 loop : -0.37 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 323 TYR 0.012 0.002 TYR C 555 PHE 0.010 0.001 PHE C 537 TRP 0.020 0.002 TRP B 583 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (22492) covalent geometry : angle 0.54272 / 0.27 (30152) hydrogen bonds : bond 0.04180 / 2.76 ( 1077) hydrogen bonds : angle 3.45873 / 2.42 ( 3111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8774.67 seconds wall clock time: 150 minutes 10.34 seconds (9010.34 seconds total)