Starting phenix.real_space_refine on Fri Oct 30 14:10:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rqu_24636/10_2026/7rqu_24636_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rqu_24636/10_2026/7rqu_24636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rqu_24636/10_2026/7rqu_24636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rqu_24636/10_2026/7rqu_24636.map" model { file = "/net/cci-nas-00/data/ceres_data/7rqu_24636/10_2026/7rqu_24636_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rqu_24636/10_2026/7rqu_24636_trim.cif" } resolution = 3.05 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= 0.140 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 S 88 5.16 5 Na 2 4.78 5 C 12500 2.51 5 N 2980 2.21 5 O 3440 1.98 5 H 16568 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35602 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 8623 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 587} Chain breaks: 5 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 6, 'ASN:plan1': 11, 'GLU:plan': 13, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 225 Chain: "C" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 8623 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 587} Chain breaks: 5 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 6, 'ASN:plan1': 11, 'GLU:plan': 13, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 225 Chain: "B" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 8623 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 587} Chain breaks: 5 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 6, 'ASN:plan1': 11, 'GLU:plan': 13, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 225 Chain: "D" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 8623 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 587} Chain breaks: 5 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 5, 'ASP:plan': 10, 'GLN:plan1': 6, 'ASN:plan1': 11, 'GLU:plan': 13, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 225 Chain: "A" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 279 Unusual residues: {' NA': 2, '6EU': 1, '6OU': 5, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, '6OU:plan-3': 1, 'YFP:plan-3': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 277 Unusual residues: {'6EU': 1, '6OU': 5, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 4, '6OU:plan-2': 1, '6OU:plan-3': 1, 'YFP:plan-3': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 277 Unusual residues: {'6EU': 1, '6OU': 5, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'YFP:plan-3': 1, '6OU:plan-1': 4, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 277 Unusual residues: {'6EU': 1, '6OU': 5, 'LBN': 2, 'YFP': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-1': 4, 'YFP:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 26 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 C 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA C 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 D 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA D 204 " occ=0.50 Time building chain proxies: 6.60, per 1000 atoms: 0.19 Number of scatterers: 35602 At special positions: 0 Unit cell: (132.84, 132.84, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 88 16.00 P 24 15.00 Na 2 11.00 O 3440 8.00 N 2980 7.00 C 12500 6.00 H 16568 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 C 386 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 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: 3.67 Conformation dependent library (CDL) restraints added in 1.3 seconds 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 65.8% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 125 through 139 removed outlier: 4.504A pdb=" N LEU A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 171 through 183 removed outlier: 4.078A pdb=" N LEU A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.514A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.081A pdb=" N LEU A 413 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 414 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 454 removed outlier: 3.596A pdb=" N ASN A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 430 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 502 through 510 removed outlier: 4.252A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 531 Processing helix chain 'A' and resid 536 through 551 removed outlier: 4.242A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.625A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.726A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 640 removed outlier: 3.787A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.519A pdb=" N PHE A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 691 through 713 Processing helix chain 'C' and resid 115 through 124 Processing helix chain 'C' and resid 125 through 139 removed outlier: 4.503A pdb=" N LEU C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 171 through 183 removed outlier: 4.078A pdb=" N LEU C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.514A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 409 through 414 removed outlier: 4.081A pdb=" N LEU C 413 " --> pdb=" O HIS C 410 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 414 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 454 removed outlier: 3.596A pdb=" N ASN C 419 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 430 " --> pdb=" O TRP C 426 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 502 through 510 removed outlier: 4.252A pdb=" N PHE C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 531 Processing helix chain 'C' and resid 536 through 551 removed outlier: 4.242A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 558 removed outlier: 3.625A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.726A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 640 removed outlier: 3.786A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 643 No H-bonds generated for 'chain 'C' and resid 641 through 643' Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.520A pdb=" N PHE C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 691 through 713 Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 125 through 139 removed outlier: 4.503A pdb=" N LEU B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 171 through 183 removed outlier: 4.078A pdb=" N LEU B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.514A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 409 through 414 removed outlier: 4.081A pdb=" N LEU B 413 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 414 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 454 removed outlier: 3.596A pdb=" N ASN B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 430 " --> pdb=" O TRP B 426 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 502 through 510 removed outlier: 4.252A pdb=" N PHE B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 531 Processing helix chain 'B' and resid 536 through 551 removed outlier: 4.242A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 removed outlier: 3.625A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.725A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 3.786A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.519A pdb=" N PHE B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 689 Processing helix chain 'B' and resid 691 through 713 Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 125 through 139 removed outlier: 4.504A pdb=" N LEU D 129 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 171 through 183 removed outlier: 4.077A pdb=" N LEU D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.514A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 409 through 414 removed outlier: 4.081A pdb=" N LEU D 413 " --> pdb=" O HIS D 410 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 414 " --> pdb=" O ASP D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 454 removed outlier: 3.596A pdb=" N ASN D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 430 " --> pdb=" O TRP D 426 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 502 through 510 removed outlier: 4.251A pdb=" N PHE D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 531 Processing helix chain 'D' and resid 536 through 551 removed outlier: 4.243A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 removed outlier: 3.625A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.725A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 3.787A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.519A pdb=" N PHE D 659 " --> pdb=" O PHE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 691 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 5.449A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 724 through 729 removed outlier: 5.285A pdb=" N LEU A 725 " --> pdb=" O CYS A 741 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N CYS A 741 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLN A 727 " --> pdb=" O ARG A 739 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG A 739 " --> pdb=" O GLN A 727 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 729 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 368 through 373 removed outlier: 5.448A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 724 through 729 removed outlier: 5.284A pdb=" N LEU C 725 " --> pdb=" O CYS C 741 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N CYS C 741 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLN C 727 " --> pdb=" O ARG C 739 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG C 739 " --> pdb=" O GLN C 727 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY C 729 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 368 through 373 removed outlier: 5.449A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 724 through 729 removed outlier: 5.284A pdb=" N LEU B 725 " --> pdb=" O CYS B 741 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N CYS B 741 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLN B 727 " --> pdb=" O ARG B 739 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG B 739 " --> pdb=" O GLN B 727 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY B 729 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 368 through 373 removed outlier: 5.449A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 724 through 729 removed outlier: 5.285A pdb=" N LEU D 725 " --> pdb=" O CYS D 741 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N CYS D 741 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLN D 727 " --> pdb=" O ARG D 739 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG D 739 " --> pdb=" O GLN D 727 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY D 729 " --> pdb=" O ASP D 737 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 3219 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: 7.45 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16544 1.03 - 1.23: 194 1.23 - 1.42: 7970 1.42 - 1.62: 11068 1.62 - 1.82: 208 Bond restraints: 35984 Sorted by residual: bond pdb=" CAS 6EU B 906 " pdb=" CAX 6EU B 906 " ideal model delta sigma weight residual 1.334 1.614 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" CAS 6EU C 901 " pdb=" CAX 6EU C 901 " ideal model delta sigma weight residual 1.334 1.613 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" CAS 6EU A 901 " pdb=" CAX 6EU A 901 " ideal model delta sigma weight residual 1.334 1.613 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" CAS 6EU D 906 " pdb=" CAX 6EU D 906 " ideal model delta sigma weight residual 1.334 1.613 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" CAW 6EU B 906 " pdb=" CBA 6EU B 906 " ideal model delta sigma weight residual 1.339 1.524 -0.185 2.00e-02 2.50e+03 8.54e+01 ... (remaining 35979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 63454 4.15 - 8.30: 335 8.30 - 12.45: 91 12.45 - 16.60: 22 16.60 - 20.75: 10 Bond angle restraints: 63912 Sorted by residual: angle pdb=" O22 YFP D 905 " pdb=" P23 YFP D 905 " pdb=" O26 YFP D 905 " ideal model delta sigma weight residual 93.19 113.94 -20.75 3.00e+00 1.11e-01 4.78e+01 angle pdb=" O22 YFP C 907 " pdb=" P23 YFP C 907 " pdb=" O26 YFP C 907 " ideal model delta sigma weight residual 93.19 113.37 -20.18 3.00e+00 1.11e-01 4.52e+01 angle pdb=" O22 YFP B 903 " pdb=" P23 YFP B 903 " pdb=" O26 YFP B 903 " ideal model delta sigma weight residual 93.19 113.36 -20.17 3.00e+00 1.11e-01 4.52e+01 angle pdb=" O22 YFP A 909 " pdb=" P23 YFP A 909 " pdb=" O26 YFP A 909 " ideal model delta sigma weight residual 93.19 112.43 -19.24 3.00e+00 1.11e-01 4.11e+01 angle pdb=" N TRP B 749 " pdb=" CA TRP B 749 " pdb=" C TRP B 749 " ideal model delta sigma weight residual 111.14 117.73 -6.59 1.08e+00 8.57e-01 3.72e+01 ... (remaining 63907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 17216 35.21 - 70.43: 635 70.43 - 105.64: 56 105.64 - 140.86: 46 140.86 - 176.07: 27 Dihedral angle restraints: 17980 sinusoidal: 9420 harmonic: 8560 Sorted by residual: dihedral pdb=" C19 6OU A 905 " pdb=" C20 6OU A 905 " pdb=" C21 6OU A 905 " pdb=" O22 6OU A 905 " ideal model delta sinusoidal sigma weight residual 301.00 124.93 176.07 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU A 903 " pdb=" C20 6OU A 903 " pdb=" O30 6OU A 903 " pdb=" C31 6OU A 903 " ideal model delta sinusoidal sigma weight residual 212.33 39.75 172.58 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C19 6OU D 908 " pdb=" C20 6OU D 908 " pdb=" O30 6OU D 908 " pdb=" C31 6OU D 908 " ideal model delta sinusoidal sigma weight residual 212.33 39.75 172.58 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 17977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2839 0.092 - 0.184: 72 0.184 - 0.276: 25 0.276 - 0.368: 20 0.368 - 0.460: 16 Chirality restraints: 2972 Sorted by residual: chirality pdb=" C2 LBN A 908 " pdb=" C1 LBN A 908 " pdb=" C3 LBN A 908 " pdb=" O7 LBN A 908 " both_signs ideal model delta sigma weight residual False -2.36 -2.82 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" C2 LBN D 907 " pdb=" C1 LBN D 907 " pdb=" C3 LBN D 907 " pdb=" O7 LBN D 907 " both_signs ideal model delta sigma weight residual False -2.36 -2.82 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" C2 LBN B 907 " pdb=" C1 LBN B 907 " pdb=" C3 LBN B 907 " pdb=" O7 LBN B 907 " both_signs ideal model delta sigma weight residual False -2.36 -2.82 0.46 2.00e-01 2.50e+01 5.27e+00 ... (remaining 2969 not shown) Planarity restraints: 5556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP B 749 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C TRP B 749 " -0.046 2.00e-02 2.50e+03 pdb=" O TRP B 749 " 0.017 2.00e-02 2.50e+03 pdb=" N THR B 750 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 749 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C TRP D 749 " 0.046 2.00e-02 2.50e+03 pdb=" O TRP D 749 " -0.017 2.00e-02 2.50e+03 pdb=" N THR D 750 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 749 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C TRP A 749 " 0.046 2.00e-02 2.50e+03 pdb=" O TRP A 749 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 750 " -0.015 2.00e-02 2.50e+03 ... (remaining 5553 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 1717 2.20 - 2.80: 67963 2.80 - 3.40: 91419 3.40 - 4.00: 119226 4.00 - 4.60: 189162 Nonbonded interactions: 469487 Sorted by model distance: nonbonded pdb=" O LEU B 553 " pdb=" HG1 THR B 556 " model vdw 1.606 2.450 nonbonded pdb=" O LEU D 553 " pdb=" HG1 THR D 556 " model vdw 1.606 2.450 nonbonded pdb=" O LEU A 553 " pdb=" HG1 THR A 556 " model vdw 1.606 2.450 nonbonded pdb=" O LEU C 553 " pdb=" HG1 THR C 556 " model vdw 1.606 2.450 nonbonded pdb=" O LEU C 588 " pdb=" HG SER C 592 " model vdw 1.708 2.450 ... (remaining 469482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 114 through 763) selection = (chain 'B' and resid 114 through 763) selection = (chain 'C' and resid 114 through 763) selection = (chain 'D' and resid 114 through 763) } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 34.020 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.280 19420 Z= 0.651 Angle : 1.211 20.748 26316 Z= 0.486 Chirality : 0.059 0.460 2972 Planarity : 0.004 0.051 3224 Dihedral : 22.657 176.070 7272 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.69 (0.18), residues: 2368 helix: 2.53 (0.14), residues: 1460 sheet: -3.29 (0.38), residues: 116 loop : -0.94 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 420 TYR 0.010 0.001 TYR C 584 PHE 0.013 0.001 PHE B 304 TRP 0.020 0.002 TRP B 749 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.01276 / 0.65 (19416) covalent geometry : angle 1.21150 / 0.49 (26308) SS BOND : bond 0.00237 / 0.12 ( 4) SS BOND : angle 0.69840 / 0.40 ( 8) hydrogen bonds : bond 0.12121 / 8.43 ( 1101) hydrogen bonds : angle 4.75797 / 3.46 ( 3219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8599 (mtm110) cc_final: 0.8290 (mtm110) REVERT: A 710 LYS cc_start: 0.7627 (ttpp) cc_final: 0.7340 (ttmt) REVERT: B 552 MET cc_start: 0.8683 (mmm) cc_final: 0.8383 (mmm) REVERT: D 581 MET cc_start: 0.8020 (mmm) cc_final: 0.7578 (mmp) REVERT: D 760 ASN cc_start: 0.7656 (t0) cc_final: 0.7448 (t0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3194 time to fit residues: 108.0015 Evaluate side-chains 185 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 0.0670 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.192500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138855 restraints weight = 52930.994| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.87 r_work: 0.3443 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19420 Z= 0.110 Angle : 0.485 5.459 26316 Z= 0.253 Chirality : 0.035 0.133 2972 Planarity : 0.003 0.037 3224 Dihedral : 23.397 179.960 3780 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.36 % Allowed : 5.28 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.96 (0.18), residues: 2368 helix: 2.83 (0.13), residues: 1468 sheet: -3.34 (0.38), residues: 116 loop : -1.03 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 420 TYR 0.009 0.001 TYR A 309 PHE 0.014 0.001 PHE D 304 TRP 0.010 0.001 TRP B 752 HIS 0.002 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (19416) covalent geometry : angle 0.48527 / 0.25 (26308) SS BOND : bond 0.00272 / 0.14 ( 4) SS BOND : angle 0.63600 / 0.37 ( 8) hydrogen bonds : bond 0.04798 / 3.40 ( 1101) hydrogen bonds : angle 3.83907 / 2.78 ( 3219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8654 (mtm110) cc_final: 0.8305 (mtm110) REVERT: B 280 ARG cc_start: 0.8583 (mtm110) cc_final: 0.8149 (mtm110) REVERT: D 581 MET cc_start: 0.8375 (mmm) cc_final: 0.8070 (mmp) outliers start: 6 outliers final: 6 residues processed: 187 average time/residue: 0.2996 time to fit residues: 85.4781 Evaluate side-chains 185 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [29, 25, 221, 189, 150, 143, 154, 232, 186, 208, 148] chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN D 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.189846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139458 restraints weight = 52904.464| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.02 r_work: 0.3421 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 19420 Z= 0.154 Angle : 0.485 4.148 26316 Z= 0.255 Chirality : 0.036 0.137 2972 Planarity : 0.003 0.049 3224 Dihedral : 21.163 179.054 3780 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.90 % Allowed : 5.46 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.77 (0.18), residues: 2368 helix: 2.66 (0.13), residues: 1468 sheet: -3.29 (0.40), residues: 116 loop : -1.08 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 420 TYR 0.012 0.001 TYR C 309 PHE 0.013 0.001 PHE C 649 TRP 0.007 0.001 TRP B 697 HIS 0.004 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (19416) covalent geometry : angle 0.48463 / 0.26 (26308) SS BOND : bond 0.00432 / 0.22 ( 4) SS BOND : angle 0.86994 / 0.50 ( 8) hydrogen bonds : bond 0.05188 / 3.68 ( 1101) hydrogen bonds : angle 3.70530 / 2.69 ( 3219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 409 ARG cc_start: 0.7378 (mtp-110) cc_final: 0.7077 (mtp-110) REVERT: D 581 MET cc_start: 0.8543 (mmm) cc_final: 0.8333 (mmp) outliers start: 15 outliers final: 14 residues processed: 188 average time/residue: 0.3151 time to fit residues: 90.6615 Evaluate side-chains 190 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [166, 172, 194, 83, 94, 32, 159, 220, 6, 10, 113] chunk 166 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN B 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.187199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133356 restraints weight = 52781.249| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.78 r_work: 0.3375 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 19420 Z= 0.246 Angle : 0.544 5.256 26316 Z= 0.287 Chirality : 0.038 0.150 2972 Planarity : 0.004 0.047 3224 Dihedral : 20.178 173.037 3780 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.50 % Allowed : 7.19 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.43 (0.18), residues: 2368 helix: 2.39 (0.14), residues: 1448 sheet: -3.29 (0.39), residues: 116 loop : -1.13 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 420 TYR 0.016 0.002 TYR A 530 PHE 0.019 0.002 PHE D 649 TRP 0.007 0.001 TRP B 697 HIS 0.006 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 (19416) covalent geometry : angle 0.54326 / 0.29 (26308) SS BOND : bond 0.00639 / 0.32 ( 4) SS BOND : angle 1.19182 / 0.68 ( 8) hydrogen bonds : bond 0.05992 / 4.26 ( 1101) hydrogen bonds : angle 3.81127 / 2.77 ( 3219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8507 (mtp180) cc_final: 0.8173 (mtm110) REVERT: B 280 ARG cc_start: 0.8579 (mtm110) cc_final: 0.8130 (mtm110) REVERT: D 748 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7517 (m-40) outliers start: 25 outliers final: 17 residues processed: 187 average time/residue: 0.3074 time to fit residues: 87.3097 Evaluate side-chains 192 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [169, 185, 47, 145, 206, 23, 194, 79, 99, 103, 208] chunk 169 optimal weight: 1.9990 chunk 185 optimal weight: 30.0000 chunk 47 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.188960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135781 restraints weight = 52599.903| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.82 r_work: 0.3415 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19420 Z= 0.155 Angle : 0.472 4.128 26316 Z= 0.251 Chirality : 0.035 0.134 2972 Planarity : 0.003 0.049 3224 Dihedral : 18.556 178.919 3780 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.44 % Allowed : 7.91 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.64 (0.18), residues: 2368 helix: 2.55 (0.14), residues: 1468 sheet: -3.25 (0.39), residues: 116 loop : -1.15 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 420 TYR 0.011 0.001 TYR A 309 PHE 0.013 0.001 PHE B 649 TRP 0.006 0.001 TRP C 697 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (19416) covalent geometry : angle 0.47210 / 0.25 (26308) SS BOND : bond 0.00445 / 0.22 ( 4) SS BOND : angle 0.99760 / 0.57 ( 8) hydrogen bonds : bond 0.05085 / 3.60 ( 1101) hydrogen bonds : angle 3.64381 / 2.64 ( 3219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8533 (mtp180) cc_final: 0.8138 (mtm110) REVERT: A 748 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7566 (m-40) REVERT: C 748 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7542 (m-40) REVERT: D 748 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7543 (m-40) outliers start: 24 outliers final: 16 residues processed: 187 average time/residue: 0.3248 time to fit residues: 91.8095 Evaluate side-chains 191 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [149, 182, 84, 45, 142, 7, 234, 153, 52, 140, 122] chunk 149 optimal weight: 1.9990 chunk 182 optimal weight: 0.0770 chunk 84 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 122 optimal weight: 0.0070 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.190272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136301 restraints weight = 52507.083| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.80 r_work: 0.3413 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 19420 Z= 0.123 Angle : 0.442 3.869 26316 Z= 0.236 Chirality : 0.034 0.125 2972 Planarity : 0.003 0.066 3224 Dihedral : 16.907 174.710 3780 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.44 % Allowed : 8.27 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.89 (0.18), residues: 2368 helix: 2.77 (0.13), residues: 1468 sheet: -3.22 (0.40), residues: 116 loop : -1.09 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 420 TYR 0.009 0.001 TYR C 511 PHE 0.010 0.001 PHE C 649 TRP 0.006 0.001 TRP C 697 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (19416) covalent geometry : angle 0.44219 / 0.24 (26308) SS BOND : bond 0.00382 / 0.19 ( 4) SS BOND : angle 0.90175 / 0.52 ( 8) hydrogen bonds : bond 0.04544 / 3.22 ( 1101) hydrogen bonds : angle 3.52061 / 2.55 ( 3219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.970 Fit side-chains REVERT: A 409 ARG cc_start: 0.7411 (mtp-110) cc_final: 0.7203 (mtp-110) REVERT: A 748 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7563 (m-40) REVERT: C 280 ARG cc_start: 0.8610 (mtm110) cc_final: 0.8143 (mtm110) REVERT: C 748 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7513 (m-40) REVERT: B 280 ARG cc_start: 0.8600 (mtm110) cc_final: 0.8148 (mtm110) REVERT: B 748 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7571 (m-40) REVERT: D 748 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7498 (m-40) outliers start: 24 outliers final: 16 residues processed: 186 average time/residue: 0.3253 time to fit residues: 91.5402 Evaluate side-chains 192 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [181, 72, 104, 133, 198, 207, 138, 219, 199, 93, 235] chunk 181 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 198 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.190043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.137054 restraints weight = 52508.149| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.77 r_work: 0.3424 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19420 Z= 0.129 Angle : 0.442 3.809 26316 Z= 0.236 Chirality : 0.034 0.128 2972 Planarity : 0.003 0.052 3224 Dihedral : 16.168 168.228 3780 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.38 % Allowed : 8.21 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.91 (0.18), residues: 2368 helix: 2.79 (0.13), residues: 1468 sheet: -3.23 (0.40), residues: 116 loop : -1.08 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 420 TYR 0.010 0.001 TYR A 511 PHE 0.011 0.001 PHE B 649 TRP 0.006 0.001 TRP C 697 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (19416) covalent geometry : angle 0.44157 / 0.24 (26308) SS BOND : bond 0.00397 / 0.20 ( 4) SS BOND : angle 0.89970 / 0.52 ( 8) hydrogen bonds : bond 0.04604 / 3.27 ( 1101) hydrogen bonds : angle 3.50843 / 2.54 ( 3219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.018 Fit side-chains REVERT: A 409 ARG cc_start: 0.7417 (mtp-110) cc_final: 0.7213 (mtp-110) REVERT: A 748 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7504 (m-40) REVERT: C 748 ASN cc_start: 0.7837 (OUTLIER) cc_final: 0.7456 (m-40) REVERT: B 748 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7550 (m-40) REVERT: D 748 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7461 (m-40) outliers start: 23 outliers final: 15 residues processed: 183 average time/residue: 0.3116 time to fit residues: 86.7063 Evaluate side-chains 191 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [118, 225, 210, 172, 81, 154, 185, 52, 198, 72, 156] chunk 118 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 185 optimal weight: 30.0000 chunk 52 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 156 optimal weight: 0.0980 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.189676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138713 restraints weight = 52437.659| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.04 r_work: 0.3400 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (18 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.003 0.023 19420 Z= 0.146 Angle : 0.457 3.920 26316 Z= 0.243 Chirality : 0.034 0.132 2972 Planarity : 0.004 0.059 3224 Dihedral : 15.689 168.367 3780 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.62 % Allowed : 7.97 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.85 (0.18), residues: 2368 helix: 2.73 (0.13), residues: 1468 sheet: -3.19 (0.40), residues: 116 loop : -1.09 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 420 TYR 0.010 0.001 TYR D 530 PHE 0.013 0.001 PHE A 649 TRP 0.005 0.001 TRP C 697 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (19416) covalent geometry : angle 0.45652 / 0.24 (26308) SS BOND : bond 0.00463 / 0.23 ( 4) SS BOND : angle 0.99050 / 0.57 ( 8) hydrogen bonds : bond 0.04811 / 3.41 ( 1101) hydrogen bonds : angle 3.53470 / 2.57 ( 3219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 748 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7422 (m-40) REVERT: C 280 ARG cc_start: 0.8619 (mtm110) cc_final: 0.8202 (mtm110) REVERT: C 748 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7409 (m-40) REVERT: B 280 ARG cc_start: 0.8618 (mtm110) cc_final: 0.8226 (mtm110) REVERT: B 748 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7413 (m-40) REVERT: D 748 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7434 (m-40) outliers start: 27 outliers final: 18 residues processed: 187 average time/residue: 0.3101 time to fit residues: 88.5010 Evaluate side-chains 193 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [25, 221, 130, 89, 141, 120, 37, 106, 69, 107, 52] chunk 25 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 120 optimal weight: 40.0000 chunk 37 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.190031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138221 restraints weight = 52191.676| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.08 r_work: 0.3410 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 19420 Z= 0.130 Angle : 0.445 3.817 26316 Z= 0.237 Chirality : 0.034 0.134 2972 Planarity : 0.004 0.058 3224 Dihedral : 15.311 168.839 3780 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.50 % Allowed : 8.21 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.92 (0.18), residues: 2368 helix: 2.80 (0.13), residues: 1468 sheet: -3.17 (0.39), residues: 116 loop : -1.09 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 420 TYR 0.009 0.001 TYR A 511 PHE 0.011 0.001 PHE B 649 TRP 0.006 0.001 TRP C 697 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (19416) covalent geometry : angle 0.44460 / 0.24 (26308) SS BOND : bond 0.00403 / 0.20 ( 4) SS BOND : angle 0.90348 / 0.52 ( 8) hydrogen bonds : bond 0.04625 / 3.28 ( 1101) hydrogen bonds : angle 3.50321 / 2.54 ( 3219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.787 Fit side-chains REVERT: A 748 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7401 (m-40) REVERT: C 280 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8209 (mtm110) REVERT: C 748 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7448 (m-40) REVERT: B 280 ARG cc_start: 0.8607 (mtm110) cc_final: 0.8201 (mtm110) REVERT: B 748 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7432 (m-40) REVERT: D 748 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7378 (m-40) outliers start: 25 outliers final: 17 residues processed: 187 average time/residue: 0.3069 time to fit residues: 87.4992 Evaluate side-chains 193 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [31, 182, 192, 77, 172, 97, 69, 34, 55, 178, 198] chunk 31 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.189091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136660 restraints weight = 52473.922| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.07 r_work: 0.3381 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19420 Z= 0.166 Angle : 0.474 4.205 26316 Z= 0.251 Chirality : 0.035 0.136 2972 Planarity : 0.004 0.060 3224 Dihedral : 15.299 168.543 3780 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.50 % Allowed : 8.33 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.77 (0.18), residues: 2368 helix: 2.68 (0.13), residues: 1468 sheet: -3.20 (0.39), residues: 116 loop : -1.13 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 420 TYR 0.012 0.001 TYR D 530 PHE 0.015 0.001 PHE A 649 TRP 0.006 0.001 TRP D 697 HIS 0.004 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (19416) covalent geometry : angle 0.47360 / 0.25 (26308) SS BOND : bond 0.00508 / 0.25 ( 4) SS BOND : angle 1.08220 / 0.62 ( 8) hydrogen bonds : bond 0.05034 / 3.57 ( 1101) hydrogen bonds : angle 3.56051 / 2.59 ( 3219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4736 Ramachandran restraints generated. 2368 Oldfield, 0 Emsley, 2368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue THR 172 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue SER 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue SER 366 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 THR 468 is missing expected H atoms. Skipping. Residue LYS 504 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 LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 754 is missing expected H atoms. Skipping. Residue VAL 756 is missing expected H atoms. Skipping. Residue ILE 758 is missing expected H atoms. Skipping. Residue ILE 759 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 748 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7368 (m-40) REVERT: C 280 ARG cc_start: 0.8644 (mtm110) cc_final: 0.8224 (mtm110) REVERT: C 748 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7447 (m-40) REVERT: B 280 ARG cc_start: 0.8619 (mtm110) cc_final: 0.8212 (mtm110) REVERT: B 748 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7480 (m-40) REVERT: D 748 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7370 (m-40) outliers start: 25 outliers final: 18 residues processed: 190 average time/residue: 0.3062 time to fit residues: 88.9060 Evaluate side-chains 197 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 748 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [125, 27, 69, 150, 231, 129, 136, 5, 213, 68, 159] chunk 125 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 213 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.190193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138405 restraints weight = 52100.556| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.06 r_work: 0.3405 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 19420 Z= 0.123 Angle : 0.443 4.469 26316 Z= 0.237 Chirality : 0.034 0.128 2972 Planarity : 0.003 0.060 3224 Dihedral : 14.915 169.396 3780 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.32 % Allowed : 8.63 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.91 (0.18), residues: 2368 helix: 2.80 (0.13), residues: 1468 sheet: -3.16 (0.39), residues: 116 loop : -1.10 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 420 TYR 0.009 0.001 TYR B 511 PHE 0.011 0.001 PHE D 649 TRP 0.006 0.001 TRP A 697 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (19416) covalent geometry : angle 0.44271 / 0.24 (26308) SS BOND : bond 0.00406 / 0.20 ( 4) SS BOND : angle 0.92270 / 0.53 ( 8) hydrogen bonds : bond 0.04591 / 3.25 ( 1101) hydrogen bonds : angle 3.51085 / 2.55 ( 3219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8420.53 seconds wall clock time: 143 minutes 14.48 seconds (8594.48 seconds total)