Starting phenix.real_space_refine on Thu Mar 5 13:04:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s88_24890/03_2026/7s88_24890.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s88_24890/03_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_24890/03_2026/7s88_24890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s88_24890/03_2026/7s88_24890.map" model { file = "/net/cci-nas-00/data/ceres_data/7s88_24890/03_2026/7s88_24890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s88_24890/03_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-5986/lib/python3.9/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: 192 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: 192 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: 192 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: 192 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: 5.02, per 1000 atoms: 0.23 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: 1.92 Conformation dependent library (CDL) restraints added in 890.5 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: 0.65 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: 3.79 Time building geometry restraints manager: 2.53 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: 13464 30.74 - 61.47: 889 61.47 - 92.20: 103 92.20 - 122.94: 16 122.94 - 153.67: 16 Dihedral angle restraints: 14488 sinusoidal: 7304 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 14485 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.950 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:7.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 19.387 153.675 9848 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 covalent geometry : bond 0.01271 (22492) covalent geometry : angle 1.47921 (30152) hydrogen bonds : bond 0.27233 ( 1077) hydrogen bonds : angle 8.31696 ( 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 : 0.544 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: 0.6392 time to fit residues: 385.4081 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 : 0.775 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 122 HIS A 174 ASN A 185 HIS A 214 GLN A 217 ASN A 369 GLN 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 546 ASN B 572 ASN C 37 ASN C 122 HIS C 174 ASN C 185 HIS C 214 GLN C 217 ASN C 369 GLN C 483 GLN ** 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 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 = 0.4056 r_free = 0.4056 target = 0.178607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127350 restraints weight = 21506.155| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.63 r_work: 0.3340 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 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 = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2040 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 : 0.586 7.822 30152 Z= 0.294 Chirality : 0.039 0.223 3232 Planarity : 0.006 0.054 3600 Dihedral : 21.159 152.429 5100 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.67 % Allowed : 11.07 % Favored : 86.26 % 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: -1.59 (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 D 555 PHE 0.012 0.001 PHE D 537 TRP 0.014 0.001 TRP B 613 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00285 (22492) covalent geometry : angle 0.58640 (30152) hydrogen bonds : bond 0.04833 ( 1077) hydrogen bonds : angle 3.99600 ( 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 434 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 377 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7651 (pt0) cc_final: 0.7152 (pm20) REVERT: A 157 CYS cc_start: 0.8223 (m) cc_final: 0.7700 (p) REVERT: A 176 GLU cc_start: 0.6704 (mt-10) cc_final: 0.5872 (mm-30) REVERT: A 177 GLU cc_start: 0.6734 (pm20) cc_final: 0.6505 (pm20) REVERT: A 234 LEU cc_start: 0.8183 (mp) cc_final: 0.7914 (mm) REVERT: A 263 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7286 (mtt90) REVERT: A 279 ASP cc_start: 0.8032 (t0) cc_final: 0.7708 (t0) REVERT: A 314 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7062 (ttmt) REVERT: A 345 MET cc_start: 0.8145 (mtm) cc_final: 0.7628 (mmm) REVERT: A 378 MET cc_start: 0.8561 (mtp) cc_final: 0.8357 (mtm) REVERT: A 618 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7876 (mp) REVERT: A 635 ASP cc_start: 0.7692 (t70) cc_final: 0.7081 (p0) REVERT: B 80 GLU cc_start: 0.7602 (pt0) cc_final: 0.7151 (pm20) REVERT: B 157 CYS cc_start: 0.8197 (m) cc_final: 0.7730 (p) REVERT: B 176 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6019 (mm-30) REVERT: B 177 GLU cc_start: 0.6755 (pm20) cc_final: 0.6538 (pm20) REVERT: B 234 LEU cc_start: 0.8134 (mp) cc_final: 0.7854 (mm) REVERT: B 263 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7429 (mtt90) REVERT: B 270 TYR cc_start: 0.8159 (t80) cc_final: 0.7842 (t80) REVERT: B 279 ASP cc_start: 0.8062 (t0) cc_final: 0.7778 (t0) REVERT: B 300 LYS cc_start: 0.7938 (mmtp) cc_final: 0.6606 (mppt) REVERT: B 635 ASP cc_start: 0.7796 (t70) cc_final: 0.7048 (p0) REVERT: C 80 GLU cc_start: 0.7648 (pt0) cc_final: 0.7133 (pm20) REVERT: C 157 CYS cc_start: 0.8232 (m) cc_final: 0.7719 (p) REVERT: C 176 GLU cc_start: 0.6688 (mt-10) cc_final: 0.5891 (mm-30) REVERT: C 177 GLU cc_start: 0.6736 (pm20) cc_final: 0.6514 (pm20) REVERT: C 234 LEU cc_start: 0.8174 (mp) cc_final: 0.7917 (mm) REVERT: C 263 ARG cc_start: 0.7957 (mtt-85) cc_final: 0.7231 (mtt90) REVERT: C 279 ASP cc_start: 0.7935 (t0) cc_final: 0.7590 (t0) REVERT: C 314 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7150 (ttmt) REVERT: C 345 MET cc_start: 0.8113 (mtm) cc_final: 0.7688 (mmm) REVERT: C 589 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7054 (ttp80) REVERT: C 618 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7840 (mp) REVERT: C 635 ASP cc_start: 0.7679 (t70) cc_final: 0.7049 (p0) REVERT: D 80 GLU cc_start: 0.7582 (pt0) cc_final: 0.7115 (pm20) REVERT: D 157 CYS cc_start: 0.8262 (m) cc_final: 0.7748 (p) REVERT: D 176 GLU cc_start: 0.6815 (mt-10) cc_final: 0.5988 (mm-30) REVERT: D 177 GLU cc_start: 0.6749 (pm20) cc_final: 0.6520 (pm20) REVERT: D 234 LEU cc_start: 0.8183 (mp) cc_final: 0.7903 (mm) REVERT: D 263 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7559 (mtt90) REVERT: D 279 ASP cc_start: 0.7986 (t0) cc_final: 0.7661 (t0) REVERT: D 300 LYS cc_start: 0.7938 (mmtp) cc_final: 0.6574 (mppt) REVERT: D 314 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7046 (ttmt) REVERT: D 345 MET cc_start: 0.8122 (mtm) cc_final: 0.7657 (mmm) REVERT: D 442 MET cc_start: 0.8355 (mtt) cc_final: 0.8144 (mtp) REVERT: D 615 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6670 (ttt180) REVERT: D 635 ASP cc_start: 0.7750 (t70) cc_final: 0.7088 (p0) outliers start: 57 outliers final: 14 residues processed: 412 average time/residue: 0.6187 time to fit residues: 290.1800 Evaluate side-chains 365 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 346 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 31 GLN 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 31 GLN 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 589 ARG 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: 6.9990 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 185 HIS B 118 GLN B 185 HIS C 118 GLN C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 185 HIS ** 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 = 0.4004 r_free = 0.4004 target = 0.173567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125289 restraints weight = 21898.457| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.55 r_work: 0.3302 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22492 Z= 0.155 Angle : 0.575 6.713 30152 Z= 0.288 Chirality : 0.040 0.183 3232 Planarity : 0.005 0.051 3600 Dihedral : 19.616 142.340 5096 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.86 % Allowed : 12.24 % Favored : 84.90 % 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: -0.06 (0.17), residues: 2448 helix: 0.63 (0.13), residues: 1504 sheet: -1.21 (0.51), residues: 88 loop : -1.00 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 323 TYR 0.013 0.002 TYR B 555 PHE 0.014 0.001 PHE B 537 TRP 0.015 0.002 TRP B 613 HIS 0.003 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00369 (22492) covalent geometry : angle 0.57519 (30152) hydrogen bonds : bond 0.04689 ( 1077) hydrogen bonds : angle 3.72697 ( 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 414 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 353 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7625 (pt0) cc_final: 0.7357 (pm20) REVERT: A 104 GLU cc_start: 0.6713 (pm20) cc_final: 0.6498 (pm20) REVERT: A 157 CYS cc_start: 0.8252 (m) cc_final: 0.7811 (p) REVERT: A 176 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6166 (mm-30) REVERT: A 177 GLU cc_start: 0.6930 (pm20) cc_final: 0.6652 (pm20) REVERT: A 234 LEU cc_start: 0.8314 (mp) cc_final: 0.7986 (mm) REVERT: A 263 ARG cc_start: 0.8180 (mtt-85) cc_final: 0.7689 (mtt90) REVERT: A 279 ASP cc_start: 0.8244 (t0) cc_final: 0.7918 (t0) REVERT: A 300 LYS cc_start: 0.8060 (mmtp) cc_final: 0.6732 (mppt) REVERT: A 314 LYS cc_start: 0.8034 (ttpt) cc_final: 0.7335 (ttmt) REVERT: A 345 MET cc_start: 0.8216 (mtm) cc_final: 0.7868 (mmm) REVERT: A 591 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: A 618 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 635 ASP cc_start: 0.7767 (t70) cc_final: 0.7091 (p0) REVERT: B 80 GLU cc_start: 0.7556 (pt0) cc_final: 0.7297 (pm20) REVERT: B 146 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7076 (mtp85) REVERT: B 157 CYS cc_start: 0.8270 (m) cc_final: 0.7869 (p) REVERT: B 176 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6102 (mm-30) REVERT: B 234 LEU cc_start: 0.8257 (mp) cc_final: 0.7896 (mm) REVERT: B 263 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7615 (mtt90) REVERT: B 279 ASP cc_start: 0.8306 (t0) cc_final: 0.7984 (t0) REVERT: B 314 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7250 (ttmt) REVERT: B 357 ASN cc_start: 0.8086 (p0) cc_final: 0.7872 (p0) REVERT: B 618 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 628 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7766 (mtp180) REVERT: B 635 ASP cc_start: 0.7682 (t70) cc_final: 0.7047 (p0) REVERT: C 80 GLU cc_start: 0.7552 (pt0) cc_final: 0.7302 (pm20) REVERT: C 157 CYS cc_start: 0.8269 (m) cc_final: 0.7825 (p) REVERT: C 176 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6147 (mm-30) REVERT: C 177 GLU cc_start: 0.6975 (pm20) cc_final: 0.6693 (pm20) REVERT: C 234 LEU cc_start: 0.8273 (mp) cc_final: 0.7952 (mm) REVERT: C 263 ARG cc_start: 0.8186 (mtt-85) cc_final: 0.7654 (mtt90) REVERT: C 279 ASP cc_start: 0.8294 (t0) cc_final: 0.7960 (t0) REVERT: C 300 LYS cc_start: 0.8044 (mmtp) cc_final: 0.6718 (mppt) REVERT: C 314 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7433 (ttmt) REVERT: C 345 MET cc_start: 0.8220 (mtm) cc_final: 0.7854 (mmm) REVERT: C 618 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7971 (mp) REVERT: C 628 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7775 (mtp180) REVERT: C 635 ASP cc_start: 0.7828 (t70) cc_final: 0.7146 (p0) REVERT: D 80 GLU cc_start: 0.7555 (pt0) cc_final: 0.7300 (pm20) REVERT: D 157 CYS cc_start: 0.8282 (m) cc_final: 0.7847 (p) REVERT: D 176 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6114 (mm-30) REVERT: D 177 GLU cc_start: 0.6901 (pm20) cc_final: 0.6656 (pm20) REVERT: D 234 LEU cc_start: 0.8283 (mp) cc_final: 0.7932 (mm) REVERT: D 263 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7643 (mtt90) REVERT: D 279 ASP cc_start: 0.8264 (t0) cc_final: 0.7935 (t0) REVERT: D 300 LYS cc_start: 0.8047 (mmtp) cc_final: 0.6714 (mppt) REVERT: D 314 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7285 (ttmt) REVERT: D 345 MET cc_start: 0.8224 (mtm) cc_final: 0.7869 (mmm) REVERT: D 442 MET cc_start: 0.8470 (mtt) cc_final: 0.8229 (mtp) REVERT: D 618 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7990 (mp) REVERT: D 628 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7758 (mtp180) REVERT: D 635 ASP cc_start: 0.7715 (t70) cc_final: 0.7078 (p0) outliers start: 61 outliers final: 17 residues processed: 382 average time/residue: 0.6434 time to fit residues: 279.0575 Evaluate side-chains 367 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 341 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 618 ILE 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 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG 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 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 452 VAL Chi-restraints excluded: chain D residue 499 VAL 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: 0.0770 chunk 150 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 194 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 369 GLN B 369 GLN C 185 HIS C 369 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 369 GLN ** 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 = 0.4042 r_free = 0.4042 target = 0.177084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130566 restraints weight = 21761.974| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.59 r_work: 0.3362 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22492 Z= 0.099 Angle : 0.496 6.120 30152 Z= 0.250 Chirality : 0.037 0.163 3232 Planarity : 0.005 0.047 3600 Dihedral : 18.547 135.689 5096 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.81 % Allowed : 12.80 % Favored : 84.38 % 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: 0.75 (0.17), residues: 2448 helix: 1.30 (0.14), residues: 1504 sheet: -1.07 (0.51), residues: 88 loop : -0.69 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 414 TYR 0.010 0.001 TYR C 555 PHE 0.011 0.001 PHE C 537 TRP 0.010 0.001 TRP A 495 HIS 0.002 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00220 (22492) covalent geometry : angle 0.49605 (30152) hydrogen bonds : bond 0.03751 ( 1077) hydrogen bonds : angle 3.52519 ( 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 399 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 339 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7635 (mtm110) cc_final: 0.6922 (mtp85) REVERT: A 157 CYS cc_start: 0.8239 (m) cc_final: 0.7942 (p) REVERT: A 176 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6132 (mm-30) REVERT: A 177 GLU cc_start: 0.6908 (pm20) cc_final: 0.6634 (pm20) REVERT: A 234 LEU cc_start: 0.8107 (mp) cc_final: 0.7838 (mm) REVERT: A 263 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7862 (mtt90) REVERT: A 279 ASP cc_start: 0.8264 (t0) cc_final: 0.7907 (t0) REVERT: A 300 LYS cc_start: 0.8037 (mmtp) cc_final: 0.6705 (mppt) REVERT: A 314 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7322 (ttmt) REVERT: A 345 MET cc_start: 0.8112 (mtm) cc_final: 0.7753 (mmm) REVERT: A 374 GLN cc_start: 0.8075 (mp-120) cc_final: 0.7771 (pm20) REVERT: A 618 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7922 (mp) REVERT: A 635 ASP cc_start: 0.7655 (t70) cc_final: 0.7007 (p0) REVERT: B 146 ARG cc_start: 0.7597 (mtm110) cc_final: 0.6962 (mtp85) REVERT: B 157 CYS cc_start: 0.8245 (m) cc_final: 0.8008 (p) REVERT: B 176 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6203 (mm-30) REVERT: B 234 LEU cc_start: 0.8134 (mp) cc_final: 0.7828 (mm) REVERT: B 263 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7837 (mtt90) REVERT: B 279 ASP cc_start: 0.8278 (t0) cc_final: 0.7929 (t0) REVERT: B 300 LYS cc_start: 0.8040 (mttm) cc_final: 0.6805 (mppt) REVERT: B 314 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7275 (ttmt) REVERT: B 323 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7850 (mpt-90) REVERT: B 357 ASN cc_start: 0.8053 (p0) cc_final: 0.7831 (p0) REVERT: B 628 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7707 (mtp180) REVERT: B 635 ASP cc_start: 0.7551 (t70) cc_final: 0.6946 (p0) REVERT: C 146 ARG cc_start: 0.7592 (mtm110) cc_final: 0.6948 (mtp85) REVERT: C 157 CYS cc_start: 0.8251 (m) cc_final: 0.7951 (p) REVERT: C 176 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6136 (mm-30) REVERT: C 177 GLU cc_start: 0.6915 (pm20) cc_final: 0.6626 (pm20) REVERT: C 234 LEU cc_start: 0.8089 (mp) cc_final: 0.7828 (mm) REVERT: C 263 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7656 (mtt90) REVERT: C 279 ASP cc_start: 0.8291 (t0) cc_final: 0.7979 (t0) REVERT: C 300 LYS cc_start: 0.8019 (mmtp) cc_final: 0.6685 (mppt) REVERT: C 314 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7309 (ttmt) REVERT: C 345 MET cc_start: 0.8057 (mtm) cc_final: 0.7744 (mmm) REVERT: C 374 GLN cc_start: 0.8074 (mp-120) cc_final: 0.7778 (pm20) REVERT: C 618 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7940 (mp) REVERT: C 635 ASP cc_start: 0.7666 (t70) cc_final: 0.7041 (p0) REVERT: D 146 ARG cc_start: 0.7582 (mtm110) cc_final: 0.6857 (mtp85) REVERT: D 157 CYS cc_start: 0.8270 (m) cc_final: 0.7957 (p) REVERT: D 176 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6025 (mm-30) REVERT: D 177 GLU cc_start: 0.6839 (pm20) cc_final: 0.6600 (pm20) REVERT: D 214 GLN cc_start: 0.7695 (mt0) cc_final: 0.7457 (mt0) REVERT: D 234 LEU cc_start: 0.8188 (mp) cc_final: 0.7873 (mm) REVERT: D 263 ARG cc_start: 0.8106 (mtt-85) cc_final: 0.7858 (mtt90) REVERT: D 279 ASP cc_start: 0.8262 (t0) cc_final: 0.7917 (t0) REVERT: D 300 LYS cc_start: 0.8019 (mmtp) cc_final: 0.6680 (mppt) REVERT: D 314 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7264 (ttmt) REVERT: D 345 MET cc_start: 0.8064 (mtm) cc_final: 0.7732 (mmm) REVERT: D 374 GLN cc_start: 0.8088 (mp-120) cc_final: 0.7792 (pm20) REVERT: D 442 MET cc_start: 0.8375 (mtt) cc_final: 0.8110 (mtp) REVERT: D 628 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7704 (mtp180) REVERT: D 635 ASP cc_start: 0.7547 (t70) cc_final: 0.6944 (p0) outliers start: 60 outliers final: 18 residues processed: 370 average time/residue: 0.6213 time to fit residues: 261.2295 Evaluate side-chains 336 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 312 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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 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 628 ARG Chi-restraints excluded: chain C residue 51 LEU 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 618 ILE Chi-restraints excluded: chain D residue 51 LEU 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 628 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 12 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 185 HIS B 185 HIS C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 185 HIS D 290 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.170760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122093 restraints weight = 21777.759| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.54 r_work: 0.3263 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22492 Z= 0.242 Angle : 0.644 7.464 30152 Z= 0.318 Chirality : 0.044 0.204 3232 Planarity : 0.005 0.051 3600 Dihedral : 18.682 130.756 5096 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.81 % Allowed : 12.95 % Favored : 84.24 % 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: 0.65 (0.17), residues: 2448 helix: 1.23 (0.13), residues: 1500 sheet: -0.97 (0.49), residues: 88 loop : -0.77 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 470 TYR 0.016 0.002 TYR B 432 PHE 0.014 0.002 PHE C 512 TRP 0.017 0.002 TRP A 613 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00597 (22492) covalent geometry : angle 0.64433 (30152) hydrogen bonds : bond 0.05179 ( 1077) hydrogen bonds : angle 3.70874 ( 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 395 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6150 (mm-30) REVERT: A 177 GLU cc_start: 0.6998 (pm20) cc_final: 0.6698 (pm20) REVERT: A 234 LEU cc_start: 0.8298 (mp) cc_final: 0.7904 (mm) REVERT: A 263 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7800 (mtt90) REVERT: A 610 ARG cc_start: 0.7744 (tpp-160) cc_final: 0.7508 (tpp-160) REVERT: A 618 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 176 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6203 (mm-30) REVERT: B 234 LEU cc_start: 0.8291 (mp) cc_final: 0.7842 (mm) REVERT: B 263 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7762 (mtt90) REVERT: B 279 ASP cc_start: 0.8407 (t0) cc_final: 0.8078 (t0) REVERT: B 323 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7947 (mmt90) REVERT: B 357 ASN cc_start: 0.8035 (p0) cc_final: 0.7835 (p0) REVERT: B 618 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8077 (mp) REVERT: B 628 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7760 (mtp180) REVERT: C 176 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6169 (mm-30) REVERT: C 177 GLU cc_start: 0.6970 (pm20) cc_final: 0.6682 (pm20) REVERT: C 214 GLN cc_start: 0.7602 (mt0) cc_final: 0.7367 (mt0) REVERT: C 234 LEU cc_start: 0.8262 (mp) cc_final: 0.7785 (mm) REVERT: C 263 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7762 (mtt90) REVERT: C 314 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7405 (ttmt) REVERT: C 610 ARG cc_start: 0.7736 (tpp-160) cc_final: 0.7512 (tpp-160) REVERT: C 618 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8018 (mp) REVERT: D 176 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6208 (mm-30) REVERT: D 214 GLN cc_start: 0.7740 (mt0) cc_final: 0.7510 (mt0) REVERT: D 234 LEU cc_start: 0.8314 (mp) cc_final: 0.7871 (mm) REVERT: D 263 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7786 (mtt90) REVERT: D 279 ASP cc_start: 0.8453 (t0) cc_final: 0.8108 (t0) REVERT: D 314 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7290 (ttmt) REVERT: D 442 MET cc_start: 0.8538 (mtt) cc_final: 0.8297 (mtp) REVERT: D 610 ARG cc_start: 0.7719 (tpp-160) cc_final: 0.7492 (tpp-160) REVERT: D 618 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8068 (mp) REVERT: D 628 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7793 (mtp180) outliers start: 60 outliers final: 27 residues processed: 357 average time/residue: 0.6115 time to fit residues: 249.2447 Evaluate side-chains 349 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 314 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 618 ILE 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 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 553 PHE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE 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 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL 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: 3.9990 chunk 44 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 369 GLN B 185 HIS B 369 GLN C 185 HIS ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.175157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127372 restraints weight = 21871.569| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.55 r_work: 0.3335 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2916 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= 0.108 Angle : 0.508 6.251 30152 Z= 0.256 Chirality : 0.038 0.189 3232 Planarity : 0.005 0.048 3600 Dihedral : 17.641 122.996 5096 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.39 % Allowed : 13.84 % Favored : 83.77 % 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: 1.01 (0.17), residues: 2448 helix: 1.54 (0.14), residues: 1508 sheet: -1.03 (0.49), residues: 88 loop : -0.67 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 323 TYR 0.011 0.001 TYR A 555 PHE 0.009 0.001 PHE D 537 TRP 0.011 0.001 TRP A 495 HIS 0.002 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00245 (22492) covalent geometry : angle 0.50824 (30152) hydrogen bonds : bond 0.03895 ( 1077) hydrogen bonds : angle 3.50720 ( 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 359 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7676 (mtm110) cc_final: 0.7008 (mtp85) REVERT: A 157 CYS cc_start: 0.8225 (m) cc_final: 0.7882 (p) REVERT: A 176 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6184 (mm-30) REVERT: A 234 LEU cc_start: 0.8263 (mp) cc_final: 0.7936 (mm) REVERT: A 263 ARG cc_start: 0.8203 (mtt-85) cc_final: 0.7765 (mtt90) REVERT: A 279 ASP cc_start: 0.8407 (t0) cc_final: 0.8080 (t0) REVERT: A 314 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7276 (ttmt) REVERT: A 345 MET cc_start: 0.8134 (mtm) cc_final: 0.7759 (mmm) REVERT: A 610 ARG cc_start: 0.7640 (tpp-160) cc_final: 0.7433 (tpp-160) REVERT: A 618 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7996 (mp) REVERT: B 146 ARG cc_start: 0.7662 (mtm110) cc_final: 0.7023 (mtp85) REVERT: B 157 CYS cc_start: 0.8218 (m) cc_final: 0.7913 (p) REVERT: B 176 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6192 (mm-30) REVERT: B 234 LEU cc_start: 0.8240 (mp) cc_final: 0.7898 (mm) REVERT: B 263 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7719 (mtt90) REVERT: B 279 ASP cc_start: 0.8428 (t0) cc_final: 0.8091 (t0) REVERT: B 314 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7229 (ttmt) REVERT: B 323 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7910 (mpt-90) REVERT: B 357 ASN cc_start: 0.8042 (p0) cc_final: 0.7824 (p0) REVERT: B 628 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7706 (mtp180) REVERT: C 146 ARG cc_start: 0.7638 (mtm110) cc_final: 0.6943 (mtp85) REVERT: C 157 CYS cc_start: 0.8238 (m) cc_final: 0.7924 (p) REVERT: C 176 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6169 (mm-30) REVERT: C 177 GLU cc_start: 0.6974 (pm20) cc_final: 0.6737 (pm20) REVERT: C 214 GLN cc_start: 0.7580 (mt0) cc_final: 0.7353 (mt0) REVERT: C 234 LEU cc_start: 0.8139 (mp) cc_final: 0.7893 (mm) REVERT: C 263 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7742 (mtt90) REVERT: C 314 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7376 (ttmt) REVERT: C 345 MET cc_start: 0.8122 (mtm) cc_final: 0.7765 (mmm) REVERT: C 610 ARG cc_start: 0.7678 (tpp-160) cc_final: 0.7470 (tpp-160) REVERT: C 618 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8020 (mp) REVERT: C 635 ASP cc_start: 0.7612 (t70) cc_final: 0.7011 (p0) REVERT: D 146 ARG cc_start: 0.7642 (mtm110) cc_final: 0.6979 (mtp85) REVERT: D 157 CYS cc_start: 0.8279 (m) cc_final: 0.7946 (p) REVERT: D 176 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6238 (mm-30) REVERT: D 234 LEU cc_start: 0.8286 (mp) cc_final: 0.7942 (mm) REVERT: D 263 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7897 (mtt90) REVERT: D 279 ASP cc_start: 0.8433 (t0) cc_final: 0.8094 (t0) REVERT: D 314 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7275 (ttmt) REVERT: D 442 MET cc_start: 0.8415 (mtt) cc_final: 0.8166 (mtp) REVERT: D 610 ARG cc_start: 0.7647 (tpp-160) cc_final: 0.7365 (tpp-160) REVERT: D 628 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7727 (mtp180) outliers start: 51 outliers final: 22 residues processed: 326 average time/residue: 0.6148 time to fit residues: 227.8448 Evaluate side-chains 330 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 300 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 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 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 D residue 51 LEU 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 628 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 165 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 237 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 185 HIS B 118 GLN C 118 GLN 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 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 = 0.4040 r_free = 0.4040 target = 0.177361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130033 restraints weight = 21806.607| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.59 r_work: 0.3347 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3098 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= 0.105 Angle : 0.496 6.422 30152 Z= 0.250 Chirality : 0.037 0.180 3232 Planarity : 0.004 0.048 3600 Dihedral : 16.576 102.948 5096 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.30 % Allowed : 14.77 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2448 helix: 1.75 (0.14), residues: 1508 sheet: -0.92 (0.52), residues: 88 loop : -0.53 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 632 TYR 0.010 0.001 TYR B 524 PHE 0.010 0.001 PHE C 537 TRP 0.011 0.001 TRP C 583 HIS 0.002 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00239 (22492) covalent geometry : angle 0.49587 (30152) hydrogen bonds : bond 0.03730 ( 1077) hydrogen bonds : angle 3.40056 ( 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 363 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 314 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7584 (mtm110) cc_final: 0.6941 (mtp85) REVERT: A 157 CYS cc_start: 0.8210 (m) cc_final: 0.7982 (p) REVERT: A 176 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6115 (mm-30) REVERT: A 177 GLU cc_start: 0.6834 (pm20) cc_final: 0.6166 (pt0) REVERT: A 234 LEU cc_start: 0.8129 (mp) cc_final: 0.7862 (mm) REVERT: A 263 ARG cc_start: 0.8149 (mtt-85) cc_final: 0.7922 (mtt90) REVERT: A 279 ASP cc_start: 0.8440 (t0) cc_final: 0.8124 (t0) REVERT: A 314 LYS cc_start: 0.7968 (ttpt) cc_final: 0.7341 (ttmt) REVERT: A 345 MET cc_start: 0.8127 (mtm) cc_final: 0.7771 (mmm) REVERT: A 618 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 146 ARG cc_start: 0.7556 (mtm110) cc_final: 0.6907 (mtp85) REVERT: B 157 CYS cc_start: 0.8234 (m) cc_final: 0.8022 (p) REVERT: B 176 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6144 (mm-30) REVERT: B 177 GLU cc_start: 0.6840 (pm20) cc_final: 0.6154 (pt0) REVERT: B 214 GLN cc_start: 0.7734 (mt0) cc_final: 0.7521 (mt0) REVERT: B 234 LEU cc_start: 0.8203 (mp) cc_final: 0.7853 (mm) REVERT: B 263 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7896 (mtt90) REVERT: B 279 ASP cc_start: 0.8356 (t0) cc_final: 0.8019 (t0) REVERT: B 300 LYS cc_start: 0.8072 (mttm) cc_final: 0.6852 (mppt) REVERT: B 314 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7306 (ttmt) REVERT: B 628 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7707 (mtp180) REVERT: C 146 ARG cc_start: 0.7556 (mtm110) cc_final: 0.6934 (mtp85) REVERT: C 176 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6204 (mm-30) REVERT: C 177 GLU cc_start: 0.6881 (pm20) cc_final: 0.6653 (pm20) REVERT: C 234 LEU cc_start: 0.8109 (mp) cc_final: 0.7813 (mm) REVERT: C 263 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7848 (mtt90) REVERT: C 314 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7353 (ttmt) REVERT: C 345 MET cc_start: 0.8126 (mtm) cc_final: 0.7792 (mmm) REVERT: C 618 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8066 (mp) REVERT: D 146 ARG cc_start: 0.7578 (mtm110) cc_final: 0.6929 (mtp85) REVERT: D 157 CYS cc_start: 0.8260 (m) cc_final: 0.8026 (p) REVERT: D 176 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6203 (mm-30) REVERT: D 177 GLU cc_start: 0.6811 (pm20) cc_final: 0.6148 (pt0) REVERT: D 214 GLN cc_start: 0.7674 (mt0) cc_final: 0.7451 (mt0) REVERT: D 234 LEU cc_start: 0.8183 (mp) cc_final: 0.7838 (mm) REVERT: D 263 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7792 (mtt90) REVERT: D 279 ASP cc_start: 0.8400 (t0) cc_final: 0.8076 (t0) REVERT: D 314 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7284 (ttmt) REVERT: D 345 MET cc_start: 0.8114 (mtm) cc_final: 0.7764 (mmm) REVERT: D 442 MET cc_start: 0.8375 (mtt) cc_final: 0.8101 (mtp) REVERT: D 610 ARG cc_start: 0.7696 (tpp-160) cc_final: 0.7442 (tpp-160) REVERT: D 628 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7751 (mtp180) outliers start: 49 outliers final: 20 residues processed: 339 average time/residue: 0.6136 time to fit residues: 237.1764 Evaluate side-chains 326 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE 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 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 28 SER Chi-restraints excluded: chain D residue 51 LEU 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 628 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 40 optimal weight: 0.5980 chunk 204 optimal weight: 6.9990 chunk 20 optimal weight: 0.0770 chunk 160 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 185 HIS A 546 ASN B 185 HIS B 546 ASN C 185 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.178860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.133754 restraints weight = 21899.352| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.56 r_work: 0.3376 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3228 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= 0.096 Angle : 0.480 6.527 30152 Z= 0.242 Chirality : 0.037 0.176 3232 Planarity : 0.004 0.049 3600 Dihedral : 16.000 88.184 5096 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.92 % Allowed : 15.38 % Favored : 82.69 % 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: 1.47 (0.18), residues: 2448 helix: 1.86 (0.14), residues: 1508 sheet: -0.82 (0.54), residues: 88 loop : -0.40 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 355 TYR 0.011 0.001 TYR C 524 PHE 0.010 0.001 PHE A 537 TRP 0.016 0.001 TRP D 583 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00214 (22492) covalent geometry : angle 0.48040 (30152) hydrogen bonds : bond 0.03536 ( 1077) hydrogen bonds : angle 3.35152 ( 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 360 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 319 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7552 (mtm110) cc_final: 0.6911 (mtp85) REVERT: A 176 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6141 (mm-30) REVERT: A 214 GLN cc_start: 0.7601 (mt0) cc_final: 0.7364 (mt0) REVERT: A 234 LEU cc_start: 0.8058 (mp) cc_final: 0.7809 (mm) REVERT: A 263 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7861 (mtt90) REVERT: A 314 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7325 (ttmt) REVERT: A 345 MET cc_start: 0.8036 (mtm) cc_final: 0.7756 (mmm) REVERT: A 578 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8557 (mtm) REVERT: B 129 ASN cc_start: 0.7828 (t0) cc_final: 0.7530 (t160) REVERT: B 146 ARG cc_start: 0.7509 (mtm110) cc_final: 0.6862 (mtp85) REVERT: B 176 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6131 (mm-30) REVERT: B 234 LEU cc_start: 0.8145 (mp) cc_final: 0.7815 (mm) REVERT: B 263 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7868 (mtt90) REVERT: B 279 ASP cc_start: 0.8437 (t0) cc_final: 0.8122 (t0) REVERT: B 300 LYS cc_start: 0.8086 (mttm) cc_final: 0.6866 (mppt) REVERT: B 314 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7295 (ttmt) REVERT: B 323 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7947 (mpt-90) REVERT: B 578 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8559 (mtm) REVERT: C 146 ARG cc_start: 0.7513 (mtm110) cc_final: 0.6870 (mtp85) REVERT: C 176 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6238 (mm-30) REVERT: C 177 GLU cc_start: 0.7003 (pm20) cc_final: 0.6779 (pm20) REVERT: C 234 LEU cc_start: 0.8053 (mp) cc_final: 0.7813 (mm) REVERT: C 263 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7828 (mtt90) REVERT: C 314 LYS cc_start: 0.7854 (ttpt) cc_final: 0.7317 (ttmt) REVERT: C 345 MET cc_start: 0.8027 (mtm) cc_final: 0.7738 (mmm) REVERT: C 635 ASP cc_start: 0.7563 (t70) cc_final: 0.7009 (p0) REVERT: D 146 ARG cc_start: 0.7527 (mtm110) cc_final: 0.6887 (mtp85) REVERT: D 176 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6237 (mm-30) REVERT: D 214 GLN cc_start: 0.7685 (mt0) cc_final: 0.7462 (mt0) REVERT: D 234 LEU cc_start: 0.8137 (mp) cc_final: 0.7813 (mm) REVERT: D 263 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7855 (mtt90) REVERT: D 279 ASP cc_start: 0.8423 (t0) cc_final: 0.8107 (t0) REVERT: D 314 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7242 (ttmt) REVERT: D 345 MET cc_start: 0.8029 (mtm) cc_final: 0.7744 (mmm) REVERT: D 442 MET cc_start: 0.8321 (mtt) cc_final: 0.8065 (mtp) REVERT: D 578 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8585 (mtm) REVERT: D 610 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.7425 (tpp-160) outliers start: 41 outliers final: 20 residues processed: 337 average time/residue: 0.6376 time to fit residues: 245.2671 Evaluate side-chains 324 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 300 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 323 ARG Chi-restraints excluded: chain B residue 410 MET 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 C residue 51 LEU 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 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 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 578 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 218 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 234 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 45 optimal weight: 0.0370 chunk 215 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS C 174 ASN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.179172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132321 restraints weight = 21828.563| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.61 r_work: 0.3378 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3326 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= 0.097 Angle : 0.486 6.518 30152 Z= 0.243 Chirality : 0.037 0.174 3232 Planarity : 0.004 0.047 3600 Dihedral : 15.568 83.269 5096 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.83 % Allowed : 15.76 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.55 (0.18), residues: 2448 helix: 1.92 (0.14), residues: 1508 sheet: -0.70 (0.55), residues: 88 loop : -0.36 (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 524 PHE 0.009 0.001 PHE C 537 TRP 0.017 0.001 TRP C 583 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00215 (22492) covalent geometry : angle 0.48554 (30152) hydrogen bonds : bond 0.03519 ( 1077) hydrogen bonds : angle 3.33198 ( 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 358 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 319 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7499 (mtm110) cc_final: 0.6841 (mtp85) REVERT: A 176 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6142 (mm-30) REVERT: A 177 GLU cc_start: 0.6826 (pm20) cc_final: 0.6059 (pt0) REVERT: A 234 LEU cc_start: 0.8006 (mp) cc_final: 0.7747 (mm) REVERT: A 263 ARG cc_start: 0.8045 (mtt-85) cc_final: 0.7833 (mtt90) REVERT: A 314 LYS cc_start: 0.7855 (ttpt) cc_final: 0.7249 (ttmt) REVERT: A 345 MET cc_start: 0.7989 (mtm) cc_final: 0.7679 (mmm) REVERT: A 578 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8555 (mtm) REVERT: B 129 ASN cc_start: 0.7751 (t0) cc_final: 0.7429 (t160) REVERT: B 146 ARG cc_start: 0.7460 (mtm110) cc_final: 0.6800 (mtp85) REVERT: B 176 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6164 (mm-30) REVERT: B 177 GLU cc_start: 0.6779 (pm20) cc_final: 0.6102 (pt0) REVERT: B 234 LEU cc_start: 0.8065 (mp) cc_final: 0.7738 (mm) REVERT: B 263 ARG cc_start: 0.8037 (mtt-85) cc_final: 0.7829 (mtt90) REVERT: B 279 ASP cc_start: 0.8413 (t0) cc_final: 0.8191 (t0) REVERT: B 300 LYS cc_start: 0.8035 (mttm) cc_final: 0.6809 (mppt) REVERT: B 314 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7213 (ttmt) REVERT: B 323 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7899 (mpt-90) REVERT: B 345 MET cc_start: 0.7999 (mtm) cc_final: 0.7688 (mmm) REVERT: B 578 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8567 (mtm) REVERT: C 146 ARG cc_start: 0.7464 (mtm110) cc_final: 0.6811 (mtp85) REVERT: C 176 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6142 (mm-30) REVERT: C 177 GLU cc_start: 0.6963 (pm20) cc_final: 0.6738 (pm20) REVERT: C 234 LEU cc_start: 0.7984 (mp) cc_final: 0.7700 (mm) REVERT: C 263 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7773 (mtt90) REVERT: C 314 LYS cc_start: 0.7810 (ttpt) cc_final: 0.7254 (ttmt) REVERT: C 345 MET cc_start: 0.7973 (mtm) cc_final: 0.7688 (mmm) REVERT: C 578 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8553 (mtm) REVERT: C 635 ASP cc_start: 0.7530 (t70) cc_final: 0.6939 (p0) REVERT: D 146 ARG cc_start: 0.7473 (mtm110) cc_final: 0.6816 (mtp85) REVERT: D 176 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6154 (mm-30) REVERT: D 177 GLU cc_start: 0.6789 (pm20) cc_final: 0.6060 (pt0) REVERT: D 214 GLN cc_start: 0.7619 (mt0) cc_final: 0.7398 (mt0) REVERT: D 234 LEU cc_start: 0.8043 (mp) cc_final: 0.7752 (mm) REVERT: D 279 ASP cc_start: 0.8425 (t0) cc_final: 0.8206 (t0) REVERT: D 314 LYS cc_start: 0.7790 (ttpt) cc_final: 0.7157 (ttmt) REVERT: D 345 MET cc_start: 0.7953 (mtm) cc_final: 0.7676 (mmm) REVERT: D 442 MET cc_start: 0.8244 (mtt) cc_final: 0.7962 (mtp) REVERT: D 578 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8562 (mtm) outliers start: 39 outliers final: 17 residues processed: 340 average time/residue: 0.6211 time to fit residues: 241.8599 Evaluate side-chains 326 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 304 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 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 323 ARG Chi-restraints excluded: chain B residue 410 MET 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 C residue 51 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 578 MET 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 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 578 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 90 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 182 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 185 HIS ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 185 HIS B 357 ASN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN ** D 369 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 = 0.4007 r_free = 0.4007 target = 0.174539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129139 restraints weight = 22056.401| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.59 r_work: 0.3303 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22492 Z= 0.166 Angle : 0.574 6.916 30152 Z= 0.286 Chirality : 0.041 0.200 3232 Planarity : 0.005 0.045 3600 Dihedral : 16.034 89.734 5096 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.74 % Allowed : 16.23 % Favored : 82.04 % 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: 1.32 (0.17), residues: 2448 helix: 1.73 (0.14), residues: 1500 sheet: -0.70 (0.52), residues: 88 loop : -0.42 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 263 TYR 0.014 0.002 TYR C 555 PHE 0.015 0.002 PHE D 553 TRP 0.022 0.002 TRP A 583 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00403 (22492) covalent geometry : angle 0.57425 (30152) hydrogen bonds : bond 0.04445 ( 1077) hydrogen bonds : angle 3.52811 ( 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 340 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7779 (t0) cc_final: 0.7463 (t160) REVERT: A 146 ARG cc_start: 0.7655 (mtm110) cc_final: 0.6969 (mtp85) REVERT: A 176 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6489 (mp0) REVERT: A 177 GLU cc_start: 0.6827 (pm20) cc_final: 0.6126 (pt0) REVERT: A 234 LEU cc_start: 0.8188 (mp) cc_final: 0.7845 (mm) REVERT: A 263 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.7907 (mtt90) REVERT: A 314 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7186 (ttmt) REVERT: A 610 ARG cc_start: 0.7621 (tpp-160) cc_final: 0.7388 (tpp-160) REVERT: B 129 ASN cc_start: 0.7799 (t0) cc_final: 0.7503 (t160) REVERT: B 146 ARG cc_start: 0.7649 (mtm110) cc_final: 0.6987 (mtp85) REVERT: B 176 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6161 (mm-30) REVERT: B 177 GLU cc_start: 0.6798 (pm20) cc_final: 0.6111 (pt0) REVERT: B 234 LEU cc_start: 0.8215 (mp) cc_final: 0.7824 (mm) REVERT: B 263 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7533 (mtt90) REVERT: B 279 ASP cc_start: 0.8435 (t0) cc_final: 0.8206 (t0) REVERT: B 314 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7215 (ttmt) REVERT: B 323 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7886 (mpt-90) REVERT: C 129 ASN cc_start: 0.7782 (t0) cc_final: 0.7461 (t160) REVERT: C 146 ARG cc_start: 0.7606 (mtm110) cc_final: 0.6950 (mtp85) REVERT: C 176 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6130 (mm-30) REVERT: C 177 GLU cc_start: 0.6940 (pm20) cc_final: 0.6731 (pm20) REVERT: C 233 ASP cc_start: 0.7821 (p0) cc_final: 0.7592 (p0) REVERT: C 234 LEU cc_start: 0.8146 (mp) cc_final: 0.7819 (mm) REVERT: C 263 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7870 (mtt90) REVERT: C 314 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7314 (ttmt) REVERT: C 610 ARG cc_start: 0.7628 (tpp-160) cc_final: 0.7402 (tpp-160) REVERT: D 129 ASN cc_start: 0.7760 (t0) cc_final: 0.7441 (t160) REVERT: D 146 ARG cc_start: 0.7620 (mtm110) cc_final: 0.6930 (mtp85) REVERT: D 176 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6153 (mm-30) REVERT: D 177 GLU cc_start: 0.6809 (pm20) cc_final: 0.6061 (pt0) REVERT: D 234 LEU cc_start: 0.8227 (mp) cc_final: 0.7805 (mm) REVERT: D 314 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7221 (ttmt) REVERT: D 442 MET cc_start: 0.8369 (mtt) cc_final: 0.8102 (mtp) outliers start: 37 outliers final: 20 residues processed: 323 average time/residue: 0.6032 time to fit residues: 223.5354 Evaluate side-chains 319 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 298 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain B residue 28 SER 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 C residue 51 LEU 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 557 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 122 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 199 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.174678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127179 restraints weight = 21877.600| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.55 r_work: 0.3309 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.004 0.031 22492 Z= 0.149 Angle : 0.553 6.721 30152 Z= 0.276 Chirality : 0.040 0.196 3232 Planarity : 0.005 0.045 3600 Dihedral : 15.929 88.719 5096 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.55 % Allowed : 16.65 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2448 helix: 1.73 (0.13), residues: 1500 sheet: -0.78 (0.51), residues: 88 loop : -0.46 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 323 TYR 0.013 0.002 TYR D 555 PHE 0.010 0.001 PHE C 537 TRP 0.022 0.002 TRP A 583 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00358 (22492) covalent geometry : angle 0.55302 (30152) hydrogen bonds : bond 0.04252 ( 1077) hydrogen bonds : angle 3.50211 ( 3111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8835.48 seconds wall clock time: 150 minutes 43.26 seconds (9043.26 seconds total)