Starting phenix.real_space_refine on Fri Mar 6 21:47:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rqw_24638/03_2026/7rqw_24638_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rqw_24638/03_2026/7rqw_24638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rqw_24638/03_2026/7rqw_24638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rqw_24638/03_2026/7rqw_24638.map" model { file = "/net/cci-nas-00/data/ceres_data/7rqw_24638/03_2026/7rqw_24638_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rqw_24638/03_2026/7rqw_24638_neut_trim.cif" } resolution = 3.11 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= 0.013 sd= 0.126 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 P 12 5.49 5 S 88 5.16 5 C 11356 2.51 5 N 2644 2.21 5 O 3080 1.98 5 H 15804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 32984 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8070 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8070 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8070 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "D" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8070 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 218 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 218 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 134 Unusual residues: {'6EU': 1, '6OU': 2, 'PCW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'6OU:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 134 Unusual residues: {'6EU': 1, '6OU': 2, 'PCW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'6OU:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA A 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA B 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA D 204 " occ=0.50 Time building chain proxies: 5.89, per 1000 atoms: 0.18 Number of scatterers: 32984 At special positions: 0 Unit cell: (119.88, 120.96, 109.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 12 15.00 O 3080 8.00 N 2644 7.00 C 11356 6.00 H 15804 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 975.8 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 67.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.619A pdb=" N ILE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.584A pdb=" N VAL A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.634A pdb=" N ALA A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.901A pdb=" N GLU A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 328' Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.550A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.654A pdb=" N TYR A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.781A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 503 through 507 removed outlier: 4.318A pdb=" N PHE A 507 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 removed outlier: 4.119A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 562 through 575 removed outlier: 4.164A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 599 removed outlier: 3.823A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 672 through 692 removed outlier: 3.687A pdb=" N ASN A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.585A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 3.788A pdb=" N PHE A 720 " --> pdb=" O MET A 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.618A pdb=" N ILE B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.585A pdb=" N VAL B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.634A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.902A pdb=" N GLU B 327 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 328' Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.550A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 3.654A pdb=" N TYR B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.781A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 503 through 507 removed outlier: 4.318A pdb=" N PHE B 507 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 4.120A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 562 through 575 removed outlier: 4.164A pdb=" N ALA B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 599 removed outlier: 3.823A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 672 through 692 removed outlier: 3.688A pdb=" N ASN B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 removed outlier: 3.585A pdb=" N LEU B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 720 removed outlier: 3.788A pdb=" N PHE B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.619A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.584A pdb=" N VAL C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.634A pdb=" N ALA C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.901A pdb=" N GLU C 327 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 328' Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.550A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.654A pdb=" N TYR C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.782A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 503 through 507 removed outlier: 4.319A pdb=" N PHE C 507 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 551 removed outlier: 4.119A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 559 Processing helix chain 'C' and resid 562 through 575 removed outlier: 4.164A pdb=" N ALA C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 removed outlier: 3.824A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 586 " --> pdb=" O PHE C 582 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 672 through 692 removed outlier: 3.687A pdb=" N ASN C 676 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 712 removed outlier: 3.585A pdb=" N LEU C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE C 712 " --> pdb=" O THR C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 720 removed outlier: 3.789A pdb=" N PHE C 720 " --> pdb=" O MET C 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.619A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.583A pdb=" N VAL D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 218 " --> pdb=" O MET D 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 221 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.635A pdb=" N ALA D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.901A pdb=" N GLU D 327 " --> pdb=" O LYS D 324 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 328 " --> pdb=" O LEU D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 328' Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.550A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 removed outlier: 3.654A pdb=" N TYR D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.782A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 503 through 507 removed outlier: 4.318A pdb=" N PHE D 507 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 4.120A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 559 Processing helix chain 'D' and resid 562 through 575 removed outlier: 4.163A pdb=" N ALA D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 599 removed outlier: 3.823A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 586 " --> pdb=" O PHE D 582 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 672 through 692 removed outlier: 3.687A pdb=" N ASN D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 712 removed outlier: 3.585A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 720 removed outlier: 3.789A pdb=" N PHE D 720 " --> pdb=" O MET D 716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 372 removed outlier: 6.848A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A 382 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 728 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 372 removed outlier: 6.848A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR B 382 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL B 728 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 368 through 372 removed outlier: 6.848A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 382 " --> pdb=" O PHE C 742 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL C 728 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 368 through 372 removed outlier: 6.848A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR D 382 " --> pdb=" O PHE D 742 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL D 728 " --> pdb=" O ASP D 737 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.16 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15784 1.02 - 1.22: 52 1.22 - 1.42: 7359 1.42 - 1.61: 10017 1.61 - 1.81: 180 Bond restraints: 33392 Sorted by residual: bond pdb=" CAS 6EU D 902 " pdb=" CAX 6EU D 902 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" CAS 6EU A 901 " pdb=" CAX 6EU A 901 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" CAS 6EU C 902 " pdb=" CAX 6EU C 902 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" CAS 6EU B 901 " pdb=" CAX 6EU B 901 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" CAW 6EU D 902 " pdb=" CBA 6EU D 902 " ideal model delta sigma weight residual 1.339 1.524 -0.185 2.00e-02 2.50e+03 8.52e+01 ... (remaining 33387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 59172 3.33 - 6.65: 388 6.65 - 9.98: 72 9.98 - 13.31: 8 13.31 - 16.63: 8 Bond angle restraints: 59648 Sorted by residual: angle pdb=" CAM 6EU A 901 " pdb=" CAV 6EU A 901 " pdb=" CBD 6EU A 901 " ideal model delta sigma weight residual 115.62 98.99 16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" CAM 6EU C 902 " pdb=" CAV 6EU C 902 " pdb=" CBD 6EU C 902 " ideal model delta sigma weight residual 115.62 98.99 16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" CAM 6EU B 901 " pdb=" CAV 6EU B 901 " pdb=" CBD 6EU B 901 " ideal model delta sigma weight residual 115.62 99.01 16.61 3.00e+00 1.11e-01 3.06e+01 angle pdb=" CAM 6EU D 902 " pdb=" CAV 6EU D 902 " pdb=" CBD 6EU D 902 " ideal model delta sigma weight residual 115.62 99.02 16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O1 LBN B 903 " pdb=" P1 LBN B 903 " pdb=" O2 LBN B 903 " ideal model delta sigma weight residual 93.45 108.96 -15.51 3.00e+00 1.11e-01 2.67e+01 ... (remaining 59643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 15816 33.92 - 67.85: 520 67.85 - 101.77: 36 101.77 - 135.70: 8 135.70 - 169.62: 8 Dihedral angle restraints: 16388 sinusoidal: 8676 harmonic: 7712 Sorted by residual: dihedral pdb=" C1 LBN A 905 " pdb=" O1 LBN A 905 " pdb=" P1 LBN A 905 " pdb=" O3 LBN A 905 " ideal model delta sinusoidal sigma weight residual 275.40 105.78 169.62 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN A 903 " pdb=" O1 LBN A 903 " pdb=" P1 LBN A 903 " pdb=" O3 LBN A 903 " ideal model delta sinusoidal sigma weight residual 275.40 105.79 169.61 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN B 906 " pdb=" O1 LBN B 906 " pdb=" P1 LBN B 906 " pdb=" O3 LBN B 906 " ideal model delta sinusoidal sigma weight residual 275.40 105.79 169.61 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 16385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2644 0.125 - 0.250: 16 0.250 - 0.375: 20 0.375 - 0.500: 4 0.500 - 0.624: 4 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CAO 6EU C 902 " pdb=" CAJ 6EU C 902 " pdb=" CAR 6EU C 902 " pdb=" CAW 6EU C 902 " both_signs ideal model delta sigma weight residual False -2.24 -2.86 0.62 2.00e-01 2.50e+01 9.75e+00 chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.86 0.62 2.00e-01 2.50e+01 9.71e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.86 0.62 2.00e-01 2.50e+01 9.66e+00 ... (remaining 2685 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 687 " 0.100 2.00e-02 2.50e+03 9.81e-02 1.44e+02 pdb=" CG ASN C 687 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 687 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN C 687 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 687 " -0.138 2.00e-02 2.50e+03 pdb="HD22 ASN C 687 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 687 " 0.100 2.00e-02 2.50e+03 9.81e-02 1.44e+02 pdb=" CG ASN B 687 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 687 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN B 687 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 687 " -0.138 2.00e-02 2.50e+03 pdb="HD22 ASN B 687 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 687 " 0.100 2.00e-02 2.50e+03 9.81e-02 1.44e+02 pdb=" CG ASN A 687 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 687 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN A 687 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 687 " -0.138 2.00e-02 2.50e+03 pdb="HD22 ASN A 687 " 0.141 2.00e-02 2.50e+03 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 2465 2.22 - 2.82: 68579 2.82 - 3.41: 85274 3.41 - 4.01: 112372 4.01 - 4.60: 176156 Nonbonded interactions: 444846 Sorted by model distance: nonbonded pdb=" O LEU D 506 " pdb=" HG SER D 510 " model vdw 1.625 2.450 nonbonded pdb=" O LEU C 506 " pdb=" HG SER C 510 " model vdw 1.625 2.450 nonbonded pdb=" O LEU B 506 " pdb=" HG SER B 510 " model vdw 1.625 2.450 nonbonded pdb=" O LEU A 506 " pdb=" HG SER A 510 " model vdw 1.625 2.450 nonbonded pdb=" HH TYR B 584 " pdb=" OG1 THR B 641 " model vdw 1.654 2.450 ... (remaining 444841 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 197 through 752 or resid 904)) selection = (chain 'B' and (resid 197 through 752 or resid 904)) selection = (chain 'C' and (resid 197 through 752 or resid 904)) selection = (chain 'D' and (resid 197 through 752 or resid 904)) } 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=0.50 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.500 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 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 : 0.011 0.268 17592 Z= 0.563 Angle : 0.994 16.631 23892 Z= 0.423 Chirality : 0.056 0.624 2688 Planarity : 0.003 0.038 2928 Dihedral : 17.954 169.620 6580 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.31 (0.18), residues: 2112 helix: 0.94 (0.14), residues: 1304 sheet: -2.12 (0.55), residues: 88 loop : -0.72 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 575 TYR 0.016 0.002 TYR D 537 PHE 0.023 0.002 PHE C 659 TRP 0.013 0.001 TRP C 549 HIS 0.002 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.01148 (17588) covalent geometry : angle 0.99415 (23884) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.21012 ( 8) hydrogen bonds : bond 0.14848 ( 972) hydrogen bonds : angle 5.56479 ( 2832) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7282 (ttpp) REVERT: A 378 HIS cc_start: 0.7408 (p90) cc_final: 0.7064 (p90) REVERT: A 445 MET cc_start: 0.7824 (mmp) cc_final: 0.7618 (mmp) REVERT: B 265 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7215 (ttpp) REVERT: B 378 HIS cc_start: 0.7417 (p90) cc_final: 0.7088 (p90) REVERT: B 445 MET cc_start: 0.7814 (mmp) cc_final: 0.7612 (mmp) REVERT: C 378 HIS cc_start: 0.7430 (p90) cc_final: 0.7141 (p90) REVERT: D 265 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7394 (ttpp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3526 time to fit residues: 96.0099 Evaluate side-chains 151 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0060 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 9.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.240922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.187992 restraints weight = 47873.970| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.80 r_work: 0.3627 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17592 Z= 0.115 Angle : 0.490 4.596 23892 Z= 0.262 Chirality : 0.033 0.123 2688 Planarity : 0.003 0.029 2928 Dihedral : 16.134 163.310 3108 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.30 % Allowed : 5.08 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.85 (0.18), residues: 2112 helix: 1.41 (0.14), residues: 1312 sheet: -2.46 (0.51), residues: 88 loop : -0.54 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 355 TYR 0.011 0.001 TYR C 565 PHE 0.014 0.001 PHE B 659 TRP 0.007 0.001 TRP B 549 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00233 (17588) covalent geometry : angle 0.49037 (23884) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.18889 ( 8) hydrogen bonds : bond 0.05010 ( 972) hydrogen bonds : angle 4.18468 ( 2832) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7654 (ttmt) cc_final: 0.7196 (ttpp) REVERT: A 378 HIS cc_start: 0.7206 (p90) cc_final: 0.6925 (p90) REVERT: A 445 MET cc_start: 0.7497 (mmp) cc_final: 0.7123 (mmp) REVERT: B 265 LYS cc_start: 0.7608 (ttmt) cc_final: 0.7131 (ttpp) REVERT: B 378 HIS cc_start: 0.7189 (p90) cc_final: 0.6924 (p90) REVERT: B 445 MET cc_start: 0.7506 (mmp) cc_final: 0.7142 (mmp) REVERT: C 378 HIS cc_start: 0.7155 (p90) cc_final: 0.6897 (p90) REVERT: C 688 LYS cc_start: 0.7501 (mptt) cc_final: 0.7060 (ttpt) REVERT: D 265 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7225 (ttpp) outliers start: 5 outliers final: 4 residues processed: 180 average time/residue: 0.3835 time to fit residues: 96.0086 Evaluate side-chains 167 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 96 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.237599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.187448 restraints weight = 47869.206| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.76 r_work: 0.3578 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17592 Z= 0.184 Angle : 0.522 4.639 23892 Z= 0.279 Chirality : 0.035 0.123 2688 Planarity : 0.003 0.031 2928 Dihedral : 15.787 162.623 3108 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.60 % Allowed : 8.01 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.61 (0.18), residues: 2112 helix: 1.29 (0.14), residues: 1312 sheet: -2.63 (0.51), residues: 88 loop : -0.76 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 575 TYR 0.015 0.002 TYR D 530 PHE 0.017 0.001 PHE D 659 TRP 0.004 0.001 TRP D 426 HIS 0.002 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00421 (17588) covalent geometry : angle 0.52208 (23884) SS BOND : bond 0.00029 ( 4) SS BOND : angle 0.18282 ( 8) hydrogen bonds : bond 0.05137 ( 972) hydrogen bonds : angle 4.17901 ( 2832) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7650 (ttmt) cc_final: 0.7195 (ttpp) REVERT: A 378 HIS cc_start: 0.7214 (p90) cc_final: 0.6916 (p90) REVERT: B 265 LYS cc_start: 0.7638 (ttmt) cc_final: 0.7186 (ttpp) REVERT: B 378 HIS cc_start: 0.7186 (p90) cc_final: 0.6907 (p90) REVERT: C 265 LYS cc_start: 0.7538 (ttmt) cc_final: 0.7056 (ttpp) REVERT: C 378 HIS cc_start: 0.7253 (p90) cc_final: 0.6983 (p90) REVERT: C 445 MET cc_start: 0.7333 (mmp) cc_final: 0.7070 (mmp) REVERT: C 478 GLU cc_start: 0.4556 (tt0) cc_final: 0.4350 (tt0) REVERT: D 265 LYS cc_start: 0.7651 (ttmt) cc_final: 0.7234 (ttpp) outliers start: 10 outliers final: 8 residues processed: 181 average time/residue: 0.3836 time to fit residues: 95.8916 Evaluate side-chains 166 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.239306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.187174 restraints weight = 47480.766| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.79 r_work: 0.3605 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17592 Z= 0.118 Angle : 0.451 4.592 23892 Z= 0.243 Chirality : 0.032 0.129 2688 Planarity : 0.003 0.031 2928 Dihedral : 15.305 161.874 3108 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.54 % Allowed : 9.93 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.89 (0.18), residues: 2112 helix: 1.53 (0.14), residues: 1312 sheet: -2.73 (0.50), residues: 88 loop : -0.67 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 428 TYR 0.009 0.001 TYR C 565 PHE 0.012 0.001 PHE D 659 TRP 0.008 0.001 TRP A 549 HIS 0.002 0.000 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00260 (17588) covalent geometry : angle 0.45119 (23884) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.21058 ( 8) hydrogen bonds : bond 0.04276 ( 972) hydrogen bonds : angle 3.90281 ( 2832) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7190 (ttpp) REVERT: B 378 HIS cc_start: 0.7140 (p90) cc_final: 0.6867 (p90) REVERT: C 265 LYS cc_start: 0.7547 (ttmt) cc_final: 0.7069 (ttpp) REVERT: C 378 HIS cc_start: 0.7206 (p90) cc_final: 0.6940 (p90) REVERT: D 265 LYS cc_start: 0.7645 (ttmt) cc_final: 0.7311 (ttpp) outliers start: 9 outliers final: 9 residues processed: 176 average time/residue: 0.3940 time to fit residues: 96.3165 Evaluate side-chains 168 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.237650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.185614 restraints weight = 47733.128| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.82 r_work: 0.3555 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17592 Z= 0.173 Angle : 0.495 4.648 23892 Z= 0.265 Chirality : 0.034 0.124 2688 Planarity : 0.003 0.031 2928 Dihedral : 15.430 163.395 3108 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.02 % Allowed : 11.42 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.72 (0.18), residues: 2112 helix: 1.40 (0.14), residues: 1312 sheet: -2.75 (0.49), residues: 88 loop : -0.75 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.015 0.002 TYR D 530 PHE 0.015 0.001 PHE D 659 TRP 0.008 0.001 TRP A 549 HIS 0.002 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00399 (17588) covalent geometry : angle 0.49527 (23884) SS BOND : bond 0.00016 ( 4) SS BOND : angle 0.17241 ( 8) hydrogen bonds : bond 0.04704 ( 972) hydrogen bonds : angle 4.00333 ( 2832) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7201 (ttpp) REVERT: B 378 HIS cc_start: 0.7177 (p90) cc_final: 0.6904 (p90) REVERT: C 265 LYS cc_start: 0.7540 (ttmt) cc_final: 0.7067 (ttpp) REVERT: C 378 HIS cc_start: 0.7254 (p90) cc_final: 0.6978 (p90) REVERT: D 265 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7318 (ttpp) outliers start: 17 outliers final: 15 residues processed: 177 average time/residue: 0.3871 time to fit residues: 94.4927 Evaluate side-chains 174 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 159 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 76 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.239546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.188403 restraints weight = 47761.705| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.78 r_work: 0.3606 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17592 Z= 0.111 Angle : 0.434 4.595 23892 Z= 0.234 Chirality : 0.032 0.125 2688 Planarity : 0.003 0.031 2928 Dihedral : 14.905 161.486 3108 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.08 % Allowed : 11.90 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.02 (0.18), residues: 2112 helix: 1.66 (0.15), residues: 1312 sheet: -2.88 (0.49), residues: 88 loop : -0.65 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 428 TYR 0.009 0.001 TYR B 309 PHE 0.012 0.001 PHE D 659 TRP 0.008 0.001 TRP B 549 HIS 0.001 0.000 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00245 (17588) covalent geometry : angle 0.43424 (23884) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.21951 ( 8) hydrogen bonds : bond 0.03997 ( 972) hydrogen bonds : angle 3.75165 ( 2832) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7644 (ttmt) cc_final: 0.7246 (ttpp) REVERT: A 309 TYR cc_start: 0.6379 (t80) cc_final: 0.6118 (t80) REVERT: B 309 TYR cc_start: 0.6385 (t80) cc_final: 0.6118 (t80) REVERT: C 378 HIS cc_start: 0.7234 (p90) cc_final: 0.6964 (p90) REVERT: D 265 LYS cc_start: 0.7646 (ttmt) cc_final: 0.7312 (ttpp) outliers start: 18 outliers final: 18 residues processed: 175 average time/residue: 0.3747 time to fit residues: 91.1172 Evaluate side-chains 178 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 27 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 201 optimal weight: 0.2980 chunk 197 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 75 optimal weight: 0.3980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.239305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.187416 restraints weight = 47544.529| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.82 r_work: 0.3600 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17592 Z= 0.118 Angle : 0.436 4.583 23892 Z= 0.234 Chirality : 0.032 0.123 2688 Planarity : 0.003 0.031 2928 Dihedral : 14.533 158.938 3108 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.14 % Allowed : 12.14 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.13 (0.19), residues: 2112 helix: 1.76 (0.15), residues: 1312 sheet: -2.87 (0.51), residues: 88 loop : -0.63 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 428 TYR 0.009 0.001 TYR C 565 PHE 0.011 0.001 PHE D 659 TRP 0.007 0.001 TRP B 549 HIS 0.001 0.000 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00264 (17588) covalent geometry : angle 0.43568 (23884) SS BOND : bond 0.00019 ( 4) SS BOND : angle 0.10028 ( 8) hydrogen bonds : bond 0.03956 ( 972) hydrogen bonds : angle 3.70386 ( 2832) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7651 (ttmt) cc_final: 0.7250 (ttpp) REVERT: A 309 TYR cc_start: 0.6378 (t80) cc_final: 0.6128 (t80) REVERT: A 359 GLU cc_start: 0.5204 (tm-30) cc_final: 0.4789 (mt-10) REVERT: D 265 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7330 (ttpp) outliers start: 19 outliers final: 18 residues processed: 181 average time/residue: 0.3980 time to fit residues: 98.3055 Evaluate side-chains 177 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 194 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.239603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.188437 restraints weight = 47268.862| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.73 r_work: 0.3615 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17592 Z= 0.109 Angle : 0.424 4.595 23892 Z= 0.228 Chirality : 0.032 0.125 2688 Planarity : 0.003 0.031 2928 Dihedral : 13.992 157.923 3108 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.02 % Allowed : 12.08 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 2112 helix: 1.84 (0.15), residues: 1312 sheet: -2.85 (0.50), residues: 88 loop : -0.57 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.009 0.001 TYR B 309 PHE 0.011 0.001 PHE D 659 TRP 0.008 0.001 TRP B 549 HIS 0.001 0.000 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00242 (17588) covalent geometry : angle 0.42380 (23884) SS BOND : bond 0.00060 ( 4) SS BOND : angle 0.26891 ( 8) hydrogen bonds : bond 0.03770 ( 972) hydrogen bonds : angle 3.62726 ( 2832) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7253 (ttpp) REVERT: A 309 TYR cc_start: 0.6381 (t80) cc_final: 0.6129 (t80) REVERT: A 359 GLU cc_start: 0.5364 (tm-30) cc_final: 0.4862 (mt-10) REVERT: B 309 TYR cc_start: 0.6380 (t80) cc_final: 0.6112 (t80) REVERT: D 265 LYS cc_start: 0.7667 (ttmt) cc_final: 0.7333 (ttpp) outliers start: 17 outliers final: 17 residues processed: 177 average time/residue: 0.3981 time to fit residues: 96.2069 Evaluate side-chains 174 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 44 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.239725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.187314 restraints weight = 47279.967| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.84 r_work: 0.3606 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17592 Z= 0.113 Angle : 0.428 7.249 23892 Z= 0.230 Chirality : 0.032 0.121 2688 Planarity : 0.003 0.030 2928 Dihedral : 13.676 156.453 3108 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.08 % Allowed : 12.08 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2112 helix: 1.90 (0.15), residues: 1308 sheet: -2.78 (0.52), residues: 88 loop : -0.58 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 428 TYR 0.009 0.001 TYR C 351 PHE 0.011 0.001 PHE D 659 TRP 0.007 0.001 TRP D 549 HIS 0.001 0.000 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00252 (17588) covalent geometry : angle 0.42827 (23884) SS BOND : bond 0.00035 ( 4) SS BOND : angle 0.06143 ( 8) hydrogen bonds : bond 0.03777 ( 972) hydrogen bonds : angle 3.61311 ( 2832) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7645 (ttmt) cc_final: 0.7250 (ttpp) REVERT: A 309 TYR cc_start: 0.6449 (t80) cc_final: 0.6193 (t80) REVERT: A 359 GLU cc_start: 0.5573 (tm-30) cc_final: 0.4906 (mt-10) REVERT: B 309 TYR cc_start: 0.6412 (t80) cc_final: 0.6140 (t80) REVERT: C 309 TYR cc_start: 0.6365 (t80) cc_final: 0.5982 (t80) REVERT: D 265 LYS cc_start: 0.7662 (ttmt) cc_final: 0.7368 (ttpp) outliers start: 18 outliers final: 17 residues processed: 179 average time/residue: 0.3888 time to fit residues: 94.8220 Evaluate side-chains 174 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 154 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.237797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.185304 restraints weight = 47690.958| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.77 r_work: 0.3593 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17592 Z= 0.159 Angle : 0.472 4.870 23892 Z= 0.253 Chirality : 0.034 0.121 2688 Planarity : 0.003 0.031 2928 Dihedral : 13.866 156.731 3108 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.08 % Allowed : 12.02 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.09 (0.19), residues: 2112 helix: 1.69 (0.15), residues: 1312 sheet: -2.82 (0.56), residues: 76 loop : -0.63 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 363 TYR 0.013 0.002 TYR D 530 PHE 0.015 0.001 PHE D 659 TRP 0.006 0.001 TRP D 549 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00367 (17588) covalent geometry : angle 0.47173 (23884) SS BOND : bond 0.00016 ( 4) SS BOND : angle 0.12880 ( 8) hydrogen bonds : bond 0.04252 ( 972) hydrogen bonds : angle 3.78601 ( 2832) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7660 (ttmt) cc_final: 0.7261 (ttpp) REVERT: A 309 TYR cc_start: 0.6451 (t80) cc_final: 0.6194 (t80) REVERT: A 359 GLU cc_start: 0.5859 (tm-30) cc_final: 0.4913 (mt-10) REVERT: B 309 TYR cc_start: 0.6469 (t80) cc_final: 0.6204 (t80) REVERT: C 309 TYR cc_start: 0.6366 (t80) cc_final: 0.5959 (t80) REVERT: D 265 LYS cc_start: 0.7676 (ttmt) cc_final: 0.7381 (ttpp) outliers start: 18 outliers final: 18 residues processed: 179 average time/residue: 0.3787 time to fit residues: 92.9012 Evaluate side-chains 179 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 85 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.238706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.186641 restraints weight = 47380.700| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.82 r_work: 0.3601 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17592 Z= 0.125 Angle : 0.441 5.282 23892 Z= 0.237 Chirality : 0.033 0.122 2688 Planarity : 0.003 0.030 2928 Dihedral : 13.453 155.903 3108 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.02 % Allowed : 12.14 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.20 (0.19), residues: 2112 helix: 1.79 (0.15), residues: 1312 sheet: -2.82 (0.57), residues: 76 loop : -0.61 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 428 TYR 0.010 0.001 TYR D 565 PHE 0.012 0.001 PHE D 659 TRP 0.008 0.001 TRP A 549 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00284 (17588) covalent geometry : angle 0.44120 (23884) SS BOND : bond 0.00012 ( 4) SS BOND : angle 0.06067 ( 8) hydrogen bonds : bond 0.03941 ( 972) hydrogen bonds : angle 3.66509 ( 2832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7749.51 seconds wall clock time: 131 minutes 45.02 seconds (7905.02 seconds total)