Starting phenix.real_space_refine on Fri Mar 6 20:03:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rqz_24641/03_2026/7rqz_24641_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rqz_24641/03_2026/7rqz_24641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rqz_24641/03_2026/7rqz_24641_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rqz_24641/03_2026/7rqz_24641_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rqz_24641/03_2026/7rqz_24641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rqz_24641/03_2026/7rqz_24641.map" } resolution = 3.32 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 11336 2.51 5 N 2624 2.21 5 O 3072 1.98 5 H 15608 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32740 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8007 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "C" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8007 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "B" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8007 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "D" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8007 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 178 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 178 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 178 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 178 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 6 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: 5.84, per 1000 atoms: 0.18 Number of scatterers: 32740 At special positions: 0 Unit cell: (121.927, 121.927, 110.058, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 12 15.00 O 3072 8.00 N 2624 7.00 C 11336 6.00 H 15608 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: 3.03 Conformation dependent library (CDL) restraints added in 913.8 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 67.5% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.673A pdb=" N ILE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 removed outlier: 3.876A pdb=" N VAL A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 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: 3.790A pdb=" N TYR A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.872A pdb=" N ARG A 363 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.028A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.949A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 505 through 510 removed outlier: 3.745A pdb=" N ASP A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 531 Processing helix chain 'A' and resid 532 through 533 No H-bonds generated for 'chain 'A' and resid 532 through 533' Processing helix chain 'A' and resid 534 through 535 No H-bonds generated for 'chain 'A' and resid 534 through 535' Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.509A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.861A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 552 through 557' Processing helix chain 'A' and resid 563 through 575 removed outlier: 4.004A pdb=" N VAL A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 599 removed outlier: 3.792A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 692 removed outlier: 3.542A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.813A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.673A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.876A pdb=" N VAL C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 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: 3.790A pdb=" N TYR C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 352 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.872A pdb=" N ARG C 363 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 408 through 413 removed outlier: 4.028A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.950A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 505 through 510 removed outlier: 3.745A pdb=" N ASP C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 531 Processing helix chain 'C' and resid 532 through 533 No H-bonds generated for 'chain 'C' and resid 532 through 533' Processing helix chain 'C' and resid 534 through 535 No H-bonds generated for 'chain 'C' and resid 534 through 535' Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.508A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR C 550 " --> pdb=" O ALA C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.861A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 552 through 557' Processing helix chain 'C' and resid 563 through 575 removed outlier: 4.004A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 removed outlier: 3.792A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 586 " --> pdb=" O PHE C 582 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 692 removed outlier: 3.542A pdb=" N MET C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 712 removed outlier: 3.813A pdb=" N PHE C 712 " --> pdb=" O THR C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.673A pdb=" N ILE B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 removed outlier: 3.876A pdb=" N VAL B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 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: 3.789A pdb=" N TYR B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.873A pdb=" N ARG B 363 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 408 through 413 removed outlier: 4.028A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.949A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 505 through 510 removed outlier: 3.746A pdb=" N ASP B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 531 Processing helix chain 'B' and resid 532 through 533 No H-bonds generated for 'chain 'B' and resid 532 through 533' Processing helix chain 'B' and resid 534 through 535 No H-bonds generated for 'chain 'B' and resid 534 through 535' Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.508A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.861A pdb=" N THR B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 557' Processing helix chain 'B' and resid 563 through 575 removed outlier: 4.004A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 599 removed outlier: 3.792A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 692 removed outlier: 3.542A pdb=" N MET B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 removed outlier: 3.813A pdb=" N PHE B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 Processing helix chain 'D' and resid 203 through 212 removed outlier: 3.673A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 removed outlier: 3.876A pdb=" N VAL D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR D 218 " --> pdb=" O MET D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 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: 3.790A pdb=" N TYR D 351 " --> pdb=" O GLY D 347 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.871A pdb=" N ARG D 363 " --> pdb=" O PRO D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 408 through 413 removed outlier: 4.028A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.950A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 505 through 510 removed outlier: 3.746A pdb=" N ASP D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 531 Processing helix chain 'D' and resid 532 through 533 No H-bonds generated for 'chain 'D' and resid 532 through 533' Processing helix chain 'D' and resid 534 through 535 No H-bonds generated for 'chain 'D' and resid 534 through 535' Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.509A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR D 550 " --> pdb=" O ALA D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.860A pdb=" N THR D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 552 through 557' Processing helix chain 'D' and resid 563 through 575 removed outlier: 4.004A pdb=" N VAL D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 599 removed outlier: 3.793A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 586 " --> pdb=" O PHE D 582 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 692 removed outlier: 3.542A pdb=" N MET D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 712 removed outlier: 3.813A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.831A pdb=" N GLU A 746 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 724 through 726 Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 378 removed outlier: 3.831A pdb=" N GLU C 746 " --> pdb=" O HIS C 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 724 through 726 Processing sheet with id=AA5, first strand: chain 'B' and resid 377 through 378 removed outlier: 3.831A pdb=" N GLU B 746 " --> pdb=" O HIS B 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 724 through 726 Processing sheet with id=AA7, first strand: chain 'D' and resid 377 through 378 removed outlier: 3.831A pdb=" N GLU D 746 " --> pdb=" O HIS D 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 724 through 726 944 hydrogen bonds defined for protein. 2796 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: 6.61 Time building geometry restraints manager: 4.06 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: 15588 1.03 - 1.23: 83 1.23 - 1.42: 7357 1.42 - 1.61: 9923 1.61 - 1.81: 189 Bond restraints: 33140 Sorted by residual: bond pdb=" CAS 6EU B 901 " pdb=" CAX 6EU B 901 " ideal model delta sigma weight residual 1.334 1.611 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" CAS 6EU A 901 " pdb=" CAX 6EU A 901 " ideal model delta sigma weight residual 1.334 1.611 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" CAS 6EU C 901 " pdb=" CAX 6EU C 901 " ideal model delta sigma weight residual 1.334 1.611 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" CAS 6EU D 902 " pdb=" CAX 6EU D 902 " ideal model delta sigma weight residual 1.334 1.610 -0.276 2.00e-02 2.50e+03 1.90e+02 bond pdb=" CAW 6EU C 901 " pdb=" CBA 6EU C 901 " ideal model delta sigma weight residual 1.339 1.524 -0.185 2.00e-02 2.50e+03 8.53e+01 ... (remaining 33135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 58836 3.68 - 7.36: 248 7.36 - 11.04: 56 11.04 - 14.72: 8 14.72 - 18.40: 8 Bond angle restraints: 59156 Sorted by residual: angle pdb=" CAM 6EU B 901 " pdb=" CAV 6EU B 901 " pdb=" CBD 6EU B 901 " ideal model delta sigma weight residual 115.62 97.22 18.40 3.00e+00 1.11e-01 3.76e+01 angle pdb=" CAM 6EU A 901 " pdb=" CAV 6EU A 901 " pdb=" CBD 6EU A 901 " ideal model delta sigma weight residual 115.62 97.23 18.39 3.00e+00 1.11e-01 3.76e+01 angle pdb=" CAM 6EU D 902 " pdb=" CAV 6EU D 902 " pdb=" CBD 6EU D 902 " ideal model delta sigma weight residual 115.62 97.23 18.39 3.00e+00 1.11e-01 3.76e+01 angle pdb=" CAM 6EU C 901 " pdb=" CAV 6EU C 901 " pdb=" CBD 6EU C 901 " ideal model delta sigma weight residual 115.62 97.25 18.37 3.00e+00 1.11e-01 3.75e+01 angle pdb=" O1 LBN C 905 " pdb=" P1 LBN C 905 " pdb=" O2 LBN C 905 " ideal model delta sigma weight residual 93.45 109.14 -15.69 3.00e+00 1.11e-01 2.74e+01 ... (remaining 59151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 15668 34.03 - 68.05: 580 68.05 - 102.08: 40 102.08 - 136.10: 8 136.10 - 170.13: 12 Dihedral angle restraints: 16308 sinusoidal: 8636 harmonic: 7672 Sorted by residual: dihedral pdb=" C1 LBN C 905 " pdb=" O1 LBN C 905 " pdb=" P1 LBN C 905 " pdb=" O3 LBN C 905 " ideal model delta sinusoidal sigma weight residual 275.40 105.27 170.13 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN B 905 " pdb=" O1 LBN B 905 " pdb=" P1 LBN B 905 " pdb=" O3 LBN B 905 " ideal model delta sinusoidal sigma weight residual 275.40 105.28 170.12 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN D 901 " pdb=" O1 LBN D 901 " pdb=" P1 LBN D 901 " pdb=" O3 LBN D 901 " ideal model delta sinusoidal sigma weight residual 275.40 105.28 170.12 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 16305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2652 0.106 - 0.213: 16 0.213 - 0.319: 4 0.319 - 0.425: 16 0.425 - 0.531: 12 Chirality restraints: 2700 Sorted by residual: chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.77 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CAO 6EU D 902 " pdb=" CAJ 6EU D 902 " pdb=" CAR 6EU D 902 " pdb=" CAW 6EU D 902 " both_signs ideal model delta sigma weight residual False -2.24 -2.77 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CAO 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAR 6EU C 901 " pdb=" CAW 6EU C 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.77 0.53 2.00e-01 2.50e+01 7.03e+00 ... (remaining 2697 not shown) Planarity restraints: 4968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 687 " -0.231 2.00e-02 2.50e+03 2.41e-01 8.70e+02 pdb=" CG ASN B 687 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 687 " 0.226 2.00e-02 2.50e+03 pdb=" ND2 ASN B 687 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 687 " 0.343 2.00e-02 2.50e+03 pdb="HD22 ASN B 687 " -0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 687 " -0.232 2.00e-02 2.50e+03 2.41e-01 8.70e+02 pdb=" CG ASN D 687 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN D 687 " 0.226 2.00e-02 2.50e+03 pdb=" ND2 ASN D 687 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN D 687 " 0.344 2.00e-02 2.50e+03 pdb="HD22 ASN D 687 " -0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 687 " 0.232 2.00e-02 2.50e+03 2.41e-01 8.70e+02 pdb=" CG ASN A 687 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 687 " -0.226 2.00e-02 2.50e+03 pdb=" ND2 ASN A 687 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 687 " -0.343 2.00e-02 2.50e+03 pdb="HD22 ASN A 687 " 0.354 2.00e-02 2.50e+03 ... (remaining 4965 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 952 2.15 - 2.76: 59631 2.76 - 3.38: 88890 3.38 - 3.99: 111067 3.99 - 4.60: 177400 Nonbonded interactions: 437940 Sorted by model distance: nonbonded pdb=" OD1 ASP C 296 " pdb="HD21 ASN C 301 " model vdw 1.541 2.450 nonbonded pdb=" OD1 ASP B 296 " pdb="HD21 ASN B 301 " model vdw 1.541 2.450 nonbonded pdb=" OD1 ASP A 296 " pdb="HD21 ASN A 301 " model vdw 1.542 2.450 nonbonded pdb=" OD1 ASP D 296 " pdb="HD21 ASN D 301 " model vdw 1.542 2.450 nonbonded pdb=" O LEU B 254 " pdb=" HG1 THR B 258 " model vdw 1.639 2.450 ... (remaining 437935 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 197 through 752 or (resid 904 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or nam \ e C38 or name C39 or name C40 or name O30 or name O32)))) selection = (chain 'B' and (resid 197 through 752 or (resid 904 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or nam \ e C38 or name C39 or name C40 or name O30 or name O32)))) selection = (chain 'C' and (resid 197 through 752 or (resid 904 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or nam \ e C38 or name C39 or name C40 or name O30 or name O32)))) selection = (chain 'D' and (resid 197 through 752 or (resid 904 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C2 \ 1 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or nam \ e C38 or name C39 or name C40 or name O30 or name O32)))) } 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.650 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.277 17536 Z= 0.558 Angle : 0.963 18.398 23820 Z= 0.388 Chirality : 0.056 0.531 2700 Planarity : 0.003 0.028 2908 Dihedral : 18.595 170.126 6564 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 2112 helix: 1.61 (0.15), residues: 1256 sheet: None (None), residues: 0 loop : -1.27 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 579 TYR 0.012 0.001 TYR A 565 PHE 0.007 0.001 PHE B 517 TRP 0.021 0.002 TRP B 697 HIS 0.003 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.01138 (17532) covalent geometry : angle 0.96282 (23812) SS BOND : bond 0.00036 ( 4) SS BOND : angle 2.12660 ( 8) hydrogen bonds : bond 0.15245 ( 944) hydrogen bonds : angle 6.03531 ( 2796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2528 time to fit residues: 75.6256 Evaluate side-chains 165 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 ASN C 687 ASN B 687 ASN D 687 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.214601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.183239 restraints weight = 50635.004| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.67 r_work: 0.3554 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17536 Z= 0.125 Angle : 0.485 4.478 23820 Z= 0.261 Chirality : 0.034 0.137 2700 Planarity : 0.003 0.029 2908 Dihedral : 17.531 164.561 3116 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2112 helix: 1.82 (0.15), residues: 1292 sheet: -2.77 (0.52), residues: 76 loop : -1.10 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 409 TYR 0.007 0.001 TYR C 401 PHE 0.007 0.001 PHE A 640 TRP 0.009 0.001 TRP C 697 HIS 0.004 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00269 (17532) covalent geometry : angle 0.48438 (23812) SS BOND : bond 0.00778 ( 4) SS BOND : angle 0.88474 ( 8) hydrogen bonds : bond 0.04968 ( 944) hydrogen bonds : angle 4.42462 ( 2796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 189 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 GLU cc_start: 0.7939 (mp0) cc_final: 0.7676 (mm-30) REVERT: C 536 GLU cc_start: 0.7971 (mp0) cc_final: 0.7688 (mm-30) REVERT: B 536 GLU cc_start: 0.7976 (mp0) cc_final: 0.7730 (mm-30) REVERT: D 536 GLU cc_start: 0.7967 (mp0) cc_final: 0.7731 (mm-30) outliers start: 4 outliers final: 0 residues processed: 189 average time/residue: 0.2587 time to fit residues: 76.6351 Evaluate side-chains 179 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 137 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.212043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.181035 restraints weight = 50899.435| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.65 r_work: 0.3527 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17536 Z= 0.183 Angle : 0.501 4.346 23820 Z= 0.266 Chirality : 0.035 0.132 2700 Planarity : 0.003 0.028 2908 Dihedral : 16.853 163.254 3116 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.24 % Allowed : 6.69 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2112 helix: 1.81 (0.14), residues: 1288 sheet: -3.03 (0.65), residues: 56 loop : -1.14 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 701 TYR 0.010 0.001 TYR B 565 PHE 0.006 0.001 PHE C 659 TRP 0.011 0.001 TRP C 697 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00428 (17532) covalent geometry : angle 0.50116 (23812) SS BOND : bond 0.00296 ( 4) SS BOND : angle 0.85629 ( 8) hydrogen bonds : bond 0.05027 ( 944) hydrogen bonds : angle 4.37239 ( 2796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 GLU cc_start: 0.8271 (mp0) cc_final: 0.8032 (mm-30) REVERT: C 536 GLU cc_start: 0.8274 (mp0) cc_final: 0.8051 (mm-30) REVERT: B 308 MET cc_start: 0.5736 (ptm) cc_final: 0.5392 (ttm) REVERT: B 536 GLU cc_start: 0.8271 (mp0) cc_final: 0.8046 (mm-30) REVERT: D 536 GLU cc_start: 0.8303 (mp0) cc_final: 0.8088 (mm-30) outliers start: 4 outliers final: 4 residues processed: 192 average time/residue: 0.2834 time to fit residues: 83.2245 Evaluate side-chains 184 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 19 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.210392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.176496 restraints weight = 50734.283| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.42 r_work: 0.3435 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 17536 Z= 0.112 Angle : 0.438 4.201 23820 Z= 0.235 Chirality : 0.033 0.124 2700 Planarity : 0.003 0.026 2908 Dihedral : 15.830 161.493 3116 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.48 % Allowed : 7.65 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.18), residues: 2112 helix: 2.08 (0.14), residues: 1296 sheet: -2.44 (0.53), residues: 76 loop : -1.11 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 432 TYR 0.007 0.001 TYR B 565 PHE 0.007 0.001 PHE D 640 TRP 0.008 0.001 TRP C 697 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00250 (17532) covalent geometry : angle 0.43790 (23812) SS BOND : bond 0.00023 ( 4) SS BOND : angle 0.81951 ( 8) hydrogen bonds : bond 0.04101 ( 944) hydrogen bonds : angle 4.05445 ( 2796) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 203 average time/residue: 0.2588 time to fit residues: 80.6005 Evaluate side-chains 192 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 123 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 180 optimal weight: 0.0010 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.205577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.168872 restraints weight = 50356.203| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.32 r_work: 0.3484 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 17536 Z= 0.154 Angle : 0.458 4.255 23820 Z= 0.245 Chirality : 0.034 0.127 2700 Planarity : 0.003 0.045 2908 Dihedral : 15.567 158.542 3116 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.60 % Allowed : 9.04 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 2112 helix: 1.90 (0.14), residues: 1320 sheet: -2.35 (0.54), residues: 76 loop : -1.31 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.010 0.001 TYR A 565 PHE 0.006 0.001 PHE C 591 TRP 0.009 0.001 TRP C 697 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00360 (17532) covalent geometry : angle 0.45773 (23812) SS BOND : bond 0.00154 ( 4) SS BOND : angle 0.68551 ( 8) hydrogen bonds : bond 0.04366 ( 944) hydrogen bonds : angle 4.07985 ( 2796) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 196 average time/residue: 0.2593 time to fit residues: 79.9368 Evaluate side-chains 189 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 49 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.207237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.169952 restraints weight = 50373.571| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.29 r_work: 0.3477 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 17536 Z= 0.098 Angle : 0.418 4.278 23820 Z= 0.225 Chirality : 0.033 0.122 2700 Planarity : 0.003 0.027 2908 Dihedral : 14.874 157.953 3116 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.60 % Allowed : 9.40 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.19), residues: 2112 helix: 2.20 (0.15), residues: 1316 sheet: -2.14 (0.56), residues: 76 loop : -1.24 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.007 0.001 TYR A 565 PHE 0.006 0.001 PHE A 640 TRP 0.009 0.001 TRP C 697 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00215 (17532) covalent geometry : angle 0.41830 (23812) SS BOND : bond 0.00028 ( 4) SS BOND : angle 0.80510 ( 8) hydrogen bonds : bond 0.03757 ( 944) hydrogen bonds : angle 3.89024 ( 2796) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 191 average time/residue: 0.2571 time to fit residues: 77.3059 Evaluate side-chains 194 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 147 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 50 optimal weight: 30.0000 chunk 152 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.212228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.185685 restraints weight = 51152.435| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.26 r_work: 0.3576 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 17536 Z= 0.165 Angle : 0.454 4.329 23820 Z= 0.243 Chirality : 0.034 0.125 2700 Planarity : 0.003 0.028 2908 Dihedral : 15.089 157.216 3116 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.78 % Allowed : 9.58 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 2112 helix: 2.06 (0.14), residues: 1316 sheet: None (None), residues: 0 loop : -1.36 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 579 TYR 0.009 0.001 TYR A 565 PHE 0.006 0.001 PHE A 659 TRP 0.010 0.001 TRP C 697 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00386 (17532) covalent geometry : angle 0.45388 (23812) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.68974 ( 8) hydrogen bonds : bond 0.04275 ( 944) hydrogen bonds : angle 4.01728 ( 2796) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 194 average time/residue: 0.2497 time to fit residues: 75.6620 Evaluate side-chains 193 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 206 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.212116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.182969 restraints weight = 51019.506| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.53 r_work: 0.3466 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17536 Z= 0.133 Angle : 0.440 4.309 23820 Z= 0.236 Chirality : 0.034 0.125 2700 Planarity : 0.003 0.037 2908 Dihedral : 14.939 157.809 3116 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.54 % Allowed : 10.06 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.18), residues: 2112 helix: 2.13 (0.15), residues: 1316 sheet: -2.04 (0.57), residues: 76 loop : -1.31 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.008 0.001 TYR D 565 PHE 0.008 0.001 PHE B 304 TRP 0.010 0.001 TRP C 697 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00304 (17532) covalent geometry : angle 0.43976 (23812) SS BOND : bond 0.00026 ( 4) SS BOND : angle 0.87942 ( 8) hydrogen bonds : bond 0.04028 ( 944) hydrogen bonds : angle 3.97463 ( 2796) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 192 average time/residue: 0.2427 time to fit residues: 73.1670 Evaluate side-chains 197 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 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 = 0.4220 r_free = 0.4220 target = 0.209080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.172609 restraints weight = 50895.440| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.34 r_work: 0.3466 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17536 Z= 0.170 Angle : 0.464 4.338 23820 Z= 0.248 Chirality : 0.035 0.126 2700 Planarity : 0.003 0.028 2908 Dihedral : 15.125 157.830 3116 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.60 % Allowed : 10.18 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.18), residues: 2112 helix: 2.02 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -1.38 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.010 0.001 TYR B 565 PHE 0.008 0.001 PHE B 304 TRP 0.010 0.001 TRP C 697 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00400 (17532) covalent geometry : angle 0.46349 (23812) SS BOND : bond 0.00007 ( 4) SS BOND : angle 0.75193 ( 8) hydrogen bonds : bond 0.04333 ( 944) hydrogen bonds : angle 4.04047 ( 2796) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 184 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 190 average time/residue: 0.2442 time to fit residues: 73.2272 Evaluate side-chains 189 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.205739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.168919 restraints weight = 50500.146| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.28 r_work: 0.3487 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 17536 Z= 0.132 Angle : 0.441 4.313 23820 Z= 0.237 Chirality : 0.034 0.125 2700 Planarity : 0.003 0.028 2908 Dihedral : 14.881 157.778 3116 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.60 % Allowed : 10.18 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.19), residues: 2112 helix: 2.13 (0.15), residues: 1316 sheet: -2.05 (0.58), residues: 76 loop : -1.34 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.009 0.001 TYR B 565 PHE 0.008 0.001 PHE D 304 TRP 0.010 0.001 TRP C 697 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00308 (17532) covalent geometry : angle 0.44111 (23812) SS BOND : bond 0.00012 ( 4) SS BOND : angle 0.90875 ( 8) hydrogen bonds : bond 0.04045 ( 944) hydrogen bonds : angle 3.96192 ( 2796) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 415 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 184 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 189 average time/residue: 0.2539 time to fit residues: 75.5861 Evaluate side-chains 193 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 390 CYS Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 66 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 209 optimal weight: 30.0000 chunk 167 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.208922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.169886 restraints weight = 51183.790| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.50 r_work: 0.3438 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 17536 Z= 0.169 Angle : 0.663 59.200 23820 Z= 0.397 Chirality : 0.034 0.205 2700 Planarity : 0.003 0.028 2908 Dihedral : 14.880 157.774 3116 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.60 % Allowed : 10.24 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.19), residues: 2112 helix: 2.14 (0.15), residues: 1316 sheet: -2.05 (0.58), residues: 76 loop : -1.34 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 355 TYR 0.008 0.001 TYR C 565 PHE 0.013 0.001 PHE A 304 TRP 0.010 0.001 TRP C 697 HIS 0.002 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00344 (17532) covalent geometry : angle 0.66269 (23812) SS BOND : bond 0.00033 ( 4) SS BOND : angle 0.86776 ( 8) hydrogen bonds : bond 0.04041 ( 944) hydrogen bonds : angle 3.96020 ( 2796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5914.13 seconds wall clock time: 101 minutes 6.52 seconds (6066.52 seconds total)