Starting phenix.real_space_refine on Mon Jul 6 01:49:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rqx_24639/07_2026/7rqx_24639_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rqx_24639/07_2026/7rqx_24639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rqx_24639/07_2026/7rqx_24639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rqx_24639/07_2026/7rqx_24639.map" model { file = "/net/cci-nas-00/data/ceres_data/7rqx_24639/07_2026/7rqx_24639_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rqx_24639/07_2026/7rqx_24639_trim.cif" } resolution = 3.36 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= 0.010 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 S 92 5.16 5 Na 2 4.78 5 C 10612 2.51 5 N 2504 2.21 5 O 2880 1.98 5 H 14344 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30450 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7413 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 4, 'PHE:plan': 2, 'TRP:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 135 Chain: "C" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7413 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 4, 'PHE:plan': 2, 'TRP:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 135 Chain: "D" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7413 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 4, 'PHE:plan': 2, 'TRP:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 135 Chain: "B" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7413 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 4, 'PHE:plan': 2, 'TRP:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 199 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'6EU': 1, '6OU': 3, 'LBN': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 199 Unusual residues: {'6EU': 1, '6OU': 3, 'LBN': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 166 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 232 Unusual residues: {'6EU': 1, '6OU': 4, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 13 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 D 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA D 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 Time building chain proxies: 4.41, per 1000 atoms: 0.14 Number of scatterers: 30450 At special positions: 0 Unit cell: (121.422, 121.422, 111.132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 92 16.00 P 16 15.00 Na 2 11.00 O 2880 8.00 N 2504 7.00 C 10612 6.00 H 14344 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=2.04 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.04 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 763.3 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 67.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.781A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 250 through 258 removed outlier: 3.723A pdb=" N THR A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.752A pdb=" N ALA A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.870A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 454 removed outlier: 3.619A pdb=" N ASN A 437 " --> pdb=" O ILE A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 502 through 504 No H-bonds generated for 'chain 'A' and resid 502 through 504' Processing helix chain 'A' and resid 505 through 510 removed outlier: 3.582A pdb=" N ASP A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 510' Processing helix chain 'A' and resid 511 through 532 removed outlier: 3.727A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 520 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.576A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 removed outlier: 3.550A pdb=" N TYR A 555 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 575 removed outlier: 3.538A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 599 removed outlier: 3.507A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.854A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.589A pdb=" N PHE A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 692 removed outlier: 3.814A pdb=" N ALA A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 712 Processing helix chain 'A' and resid 712 through 717 Processing helix chain 'C' and resid 204 through 211 removed outlier: 3.781A pdb=" N ILE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 223 Processing helix chain 'C' and resid 250 through 258 removed outlier: 3.723A pdb=" N THR C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.753A pdb=" N ALA C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.870A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 454 removed outlier: 3.619A pdb=" N ASN C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 502 through 504 No H-bonds generated for 'chain 'C' and resid 502 through 504' Processing helix chain 'C' and resid 505 through 510 removed outlier: 3.582A pdb=" N ASP C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER C 510 " --> pdb=" O LEU C 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 505 through 510' Processing helix chain 'C' and resid 511 through 532 removed outlier: 3.728A pdb=" N LEU C 515 " --> pdb=" O TYR C 511 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 520 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.576A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 559 removed outlier: 3.549A pdb=" N TYR C 555 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 556 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 575 removed outlier: 3.538A pdb=" N GLU C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 removed outlier: 3.506A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.854A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.590A pdb=" N PHE C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 692 removed outlier: 3.814A pdb=" N ALA C 680 " --> pdb=" O ASN C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 712 Processing helix chain 'C' and resid 712 through 717 Processing helix chain 'D' and resid 204 through 211 removed outlier: 3.782A pdb=" N ILE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 223 Processing helix chain 'D' and resid 250 through 258 removed outlier: 3.723A pdb=" N THR D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.752A pdb=" N ALA D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.870A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 454 removed outlier: 3.619A pdb=" N ASN D 437 " --> pdb=" O ILE D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 502 through 504 No H-bonds generated for 'chain 'D' and resid 502 through 504' Processing helix chain 'D' and resid 505 through 510 removed outlier: 3.583A pdb=" N ASP D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER D 510 " --> pdb=" O LEU D 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 505 through 510' Processing helix chain 'D' and resid 511 through 532 removed outlier: 3.727A pdb=" N LEU D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE D 516 " --> pdb=" O SER D 512 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 520 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.576A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 559 removed outlier: 3.550A pdb=" N TYR D 555 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 556 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 575 removed outlier: 3.538A pdb=" N GLU D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 599 removed outlier: 3.507A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.855A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.588A pdb=" N PHE D 659 " --> pdb=" O PHE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 692 removed outlier: 3.814A pdb=" N ALA D 680 " --> pdb=" O ASN D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 712 Processing helix chain 'D' and resid 712 through 717 Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.781A pdb=" N ILE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.722A pdb=" N THR B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.752A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.870A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 3.619A pdb=" N ASN B 437 " --> pdb=" O ILE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 502 through 504 No H-bonds generated for 'chain 'B' and resid 502 through 504' Processing helix chain 'B' and resid 505 through 510 removed outlier: 3.583A pdb=" N ASP B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 505 through 510' Processing helix chain 'B' and resid 511 through 532 removed outlier: 3.726A pdb=" N LEU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 520 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.576A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.549A pdb=" N TYR B 555 " --> pdb=" O MET B 552 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 removed outlier: 3.538A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 599 removed outlier: 3.506A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.855A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.588A pdb=" N PHE B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 692 removed outlier: 3.814A pdb=" N ALA B 680 " --> pdb=" O ASN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 717 Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 373 removed outlier: 3.955A pdb=" N GLU A 371 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 382 " --> pdb=" O PHE A 742 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 369 through 373 removed outlier: 3.955A pdb=" N GLU C 371 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 382 " --> pdb=" O PHE C 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 369 through 373 removed outlier: 3.955A pdb=" N GLU D 371 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 382 " --> pdb=" O PHE D 742 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 369 through 373 removed outlier: 3.955A pdb=" N GLU B 371 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 382 " --> pdb=" O PHE B 742 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2595 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: 5.31 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14316 1.02 - 1.22: 75 1.22 - 1.41: 6843 1.41 - 1.61: 9381 1.61 - 1.81: 201 Bond restraints: 30816 Sorted by residual: bond pdb=" CAS 6EU C 904 " pdb=" CAX 6EU C 904 " ideal model delta sigma weight residual 1.334 1.612 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" CAS 6EU D 905 " pdb=" CAX 6EU D 905 " ideal model delta sigma weight residual 1.334 1.612 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" CAS 6EU B 907 " pdb=" CAX 6EU B 907 " ideal model delta sigma weight residual 1.334 1.612 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" CAS 6EU A 903 " pdb=" CAX 6EU A 903 " ideal model delta sigma weight residual 1.334 1.612 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" CAW 6EU C 904 " pdb=" CBA 6EU C 904 " ideal model delta sigma weight residual 1.339 1.520 -0.181 2.00e-02 2.50e+03 8.16e+01 ... (remaining 30811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.89: 54708 5.89 - 11.79: 88 11.79 - 17.68: 12 17.68 - 23.57: 8 23.57 - 29.47: 16 Bond angle restraints: 54832 Sorted by residual: angle pdb=" CG1 ILE D 679 " pdb=" CD1 ILE D 679 " pdb="HD11 ILE D 679 " ideal model delta sigma weight residual 109.00 79.53 29.47 3.00e+00 1.11e-01 9.65e+01 angle pdb=" CG1 ILE C 679 " pdb=" CD1 ILE C 679 " pdb="HD11 ILE C 679 " ideal model delta sigma weight residual 109.00 79.54 29.46 3.00e+00 1.11e-01 9.65e+01 angle pdb=" CG1 ILE A 679 " pdb=" CD1 ILE A 679 " pdb="HD11 ILE A 679 " ideal model delta sigma weight residual 109.00 79.56 29.44 3.00e+00 1.11e-01 9.63e+01 angle pdb=" CG1 ILE C 679 " pdb=" CD1 ILE C 679 " pdb="HD13 ILE C 679 " ideal model delta sigma weight residual 109.00 79.56 29.44 3.00e+00 1.11e-01 9.63e+01 angle pdb=" CG1 ILE B 679 " pdb=" CD1 ILE B 679 " pdb="HD11 ILE B 679 " ideal model delta sigma weight residual 109.00 79.59 29.41 3.00e+00 1.11e-01 9.61e+01 ... (remaining 54827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 14760 35.29 - 70.58: 492 70.58 - 105.86: 36 105.86 - 141.15: 12 141.15 - 176.44: 8 Dihedral angle restraints: 15308 sinusoidal: 8020 harmonic: 7288 Sorted by residual: dihedral pdb=" C1 LBN C 901 " pdb=" O1 LBN C 901 " pdb=" P1 LBN C 901 " pdb=" O3 LBN C 901 " ideal model delta sinusoidal sigma weight residual 275.40 98.96 176.44 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN D 903 " pdb=" O1 LBN D 903 " pdb=" P1 LBN D 903 " pdb=" O3 LBN D 903 " ideal model delta sinusoidal sigma weight residual 275.40 98.98 176.42 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN A 901 " pdb=" O1 LBN A 901 " pdb=" P1 LBN A 901 " pdb=" O3 LBN A 901 " ideal model delta sinusoidal sigma weight residual 275.40 99.02 176.38 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 15305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2399 0.094 - 0.187: 77 0.187 - 0.281: 12 0.281 - 0.374: 13 0.374 - 0.468: 23 Chirality restraints: 2524 Sorted by residual: chirality pdb=" C2 LBN A 905 " pdb=" C1 LBN A 905 " pdb=" C3 LBN A 905 " pdb=" O7 LBN A 905 " both_signs ideal model delta sigma weight residual False -2.36 -2.83 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" C2 LBN B 902 " pdb=" C1 LBN B 902 " pdb=" C3 LBN B 902 " pdb=" O7 LBN B 902 " both_signs ideal model delta sigma weight residual False -2.36 -2.83 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C2 LBN D 902 " pdb=" C1 LBN D 902 " pdb=" C3 LBN D 902 " pdb=" O7 LBN D 902 " both_signs ideal model delta sigma weight residual False -2.36 -2.83 0.47 2.00e-01 2.50e+01 5.46e+00 ... (remaining 2521 not shown) Planarity restraints: 4680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 403 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.32e+00 pdb=" C SER B 403 " 0.047 2.00e-02 2.50e+03 pdb=" O SER B 403 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 404 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 403 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C SER A 403 " 0.047 2.00e-02 2.50e+03 pdb=" O SER A 403 " -0.017 2.00e-02 2.50e+03 pdb=" N SER A 404 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 403 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C SER D 403 " 0.046 2.00e-02 2.50e+03 pdb=" O SER D 403 " -0.017 2.00e-02 2.50e+03 pdb=" N SER D 404 " -0.016 2.00e-02 2.50e+03 ... (remaining 4677 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 605 2.12 - 2.74: 51334 2.74 - 3.36: 84895 3.36 - 3.98: 104114 3.98 - 4.60: 166569 Nonbonded interactions: 407517 Sorted by model distance: nonbonded pdb=" OE2 GLU C 600 " pdb="HH22 ARG D 455 " model vdw 1.501 2.450 nonbonded pdb="HH22 ARG C 455 " pdb=" OE2 GLU B 600 " model vdw 1.558 2.450 nonbonded pdb="HH22 ARG A 455 " pdb=" OE2 GLU D 600 " model vdw 1.560 2.450 nonbonded pdb=" OE2 GLU A 600 " pdb="HH22 ARG B 455 " model vdw 1.653 2.450 nonbonded pdb=" OE2 GLU D 326 " pdb="HH12 ARG D 355 " model vdw 1.654 2.450 ... (remaining 407512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 203 through 752) selection = (chain 'B' and resid 203 through 752) selection = (chain 'C' and resid 203 through 752) selection = (chain 'D' and resid 203 through 752) } 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: 1.400 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: 0.210 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.060 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.012 0.278 16476 Z= 0.602 Angle : 1.058 16.769 22380 Z= 0.464 Chirality : 0.062 0.468 2524 Planarity : 0.005 0.094 2736 Dihedral : 19.015 176.441 6144 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1992 helix: 0.66 (0.16), residues: 1204 sheet: -2.16 (0.60), residues: 56 loop : -1.43 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 701 TYR 0.013 0.001 TYR D 401 PHE 0.028 0.001 PHE C 473 TRP 0.011 0.001 TRP D 697 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.01187 / 0.60 (16472) covalent geometry : angle 1.05845 / 0.46 (22372) SS BOND : bond 0.00417 / 0.20 ( 4) SS BOND : angle 0.87234 / 0.47 ( 8) hydrogen bonds : bond 0.15580 / 10.96 ( 885) hydrogen bonds : angle 5.96099 / 4.34 ( 2595) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 GLN cc_start: 0.8516 (pp30) cc_final: 0.8160 (pp30) REVERT: C 443 LEU cc_start: 0.7998 (tt) cc_final: 0.7648 (tp) REVERT: D 519 GLN cc_start: 0.8557 (pp30) cc_final: 0.8207 (pp30) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2179 time to fit residues: 72.9480 Evaluate side-chains 165 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0000 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 HIS C 364 HIS C 423 GLN D 364 HIS D 423 GLN B 364 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.189355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146842 restraints weight = 54249.072| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.32 r_work: 0.3312 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16476 Z= 0.136 Angle : 0.515 4.318 22380 Z= 0.275 Chirality : 0.035 0.138 2524 Planarity : 0.004 0.072 2736 Dihedral : 18.229 179.818 3068 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.07 % Allowed : 7.95 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.03 (0.19), residues: 1992 helix: 0.97 (0.15), residues: 1212 sheet: -1.84 (0.56), residues: 56 loop : -1.45 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 701 TYR 0.014 0.001 TYR D 309 PHE 0.021 0.001 PHE D 473 TRP 0.011 0.001 TRP A 697 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (16472) covalent geometry : angle 0.51462 / 0.28 (22372) SS BOND : bond 0.00193 / 0.09 ( 4) SS BOND : angle 0.48587 / 0.26 ( 8) hydrogen bonds : bond 0.04471 / 3.17 ( 885) hydrogen bonds : angle 4.71941 / 3.44 ( 2595) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8730 (tmm) cc_final: 0.8392 (tmm) REVERT: A 423 GLN cc_start: 0.8673 (tp40) cc_final: 0.8329 (tp-100) REVERT: A 749 TRP cc_start: 0.5056 (OUTLIER) cc_final: 0.4797 (t-100) REVERT: C 308 MET cc_start: 0.8578 (tmm) cc_final: 0.8283 (tmm) REVERT: C 443 LEU cc_start: 0.8489 (tt) cc_final: 0.8188 (tp) REVERT: C 631 TYR cc_start: 0.7887 (t80) cc_final: 0.7623 (t80) REVERT: D 631 TYR cc_start: 0.8027 (t80) cc_final: 0.7743 (t80) REVERT: B 457 VAL cc_start: 0.8494 (m) cc_final: 0.8086 (t) outliers start: 16 outliers final: 8 residues processed: 180 average time/residue: 0.2087 time to fit residues: 59.3511 Evaluate side-chains 167 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 83 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 HIS C 423 GLN D 364 HIS D 423 GLN B 364 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.187308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143992 restraints weight = 54075.909| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.40 r_work: 0.3277 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16476 Z= 0.158 Angle : 0.491 5.024 22380 Z= 0.262 Chirality : 0.034 0.139 2524 Planarity : 0.004 0.068 2736 Dihedral : 16.965 178.797 3068 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.34 % Allowed : 9.16 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1992 helix: 1.18 (0.15), residues: 1224 sheet: -1.82 (0.53), residues: 56 loop : -1.34 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 701 TYR 0.014 0.001 TYR A 309 PHE 0.019 0.001 PHE A 473 TRP 0.010 0.001 TRP D 697 HIS 0.007 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (16472) covalent geometry : angle 0.49111 / 0.26 (22372) SS BOND : bond 0.00123 / 0.06 ( 4) SS BOND : angle 0.50368 / 0.27 ( 8) hydrogen bonds : bond 0.03957 / 2.82 ( 885) hydrogen bonds : angle 4.44514 / 3.22 ( 2595) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8777 (tmm) cc_final: 0.8391 (tmm) REVERT: A 423 GLN cc_start: 0.8676 (tp40) cc_final: 0.8318 (tp-100) REVERT: A 644 MET cc_start: 0.7614 (ptt) cc_final: 0.7272 (ptt) REVERT: A 749 TRP cc_start: 0.5062 (OUTLIER) cc_final: 0.4805 (t-100) REVERT: C 308 MET cc_start: 0.8610 (tmm) cc_final: 0.8270 (tmm) REVERT: C 473 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6904 (m-80) REVERT: C 644 MET cc_start: 0.7691 (ptt) cc_final: 0.7356 (ptt) REVERT: C 749 TRP cc_start: 0.4919 (OUTLIER) cc_final: 0.4696 (t-100) REVERT: D 644 MET cc_start: 0.7632 (ptt) cc_final: 0.7290 (ptt) REVERT: B 457 VAL cc_start: 0.8480 (m) cc_final: 0.8043 (t) REVERT: B 644 MET cc_start: 0.7644 (ptt) cc_final: 0.7285 (ptt) outliers start: 20 outliers final: 8 residues processed: 171 average time/residue: 0.2335 time to fit residues: 62.8228 Evaluate side-chains 166 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 749 TRP Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain B residue 364 HIS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 193 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 364 HIS D 423 GLN B 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.187516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.144448 restraints weight = 53529.004| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.35 r_work: 0.3277 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16476 Z= 0.138 Angle : 0.471 6.902 22380 Z= 0.254 Chirality : 0.034 0.158 2524 Planarity : 0.004 0.063 2736 Dihedral : 16.178 172.441 3068 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.40 % Allowed : 9.83 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.55 (0.19), residues: 1992 helix: 1.39 (0.16), residues: 1224 sheet: -1.74 (0.54), residues: 56 loop : -1.28 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 701 TYR 0.015 0.001 TYR A 309 PHE 0.015 0.001 PHE A 473 TRP 0.009 0.001 TRP D 697 HIS 0.007 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (16472) covalent geometry : angle 0.47147 / 0.25 (22372) SS BOND : bond 0.00090 / 0.04 ( 4) SS BOND : angle 0.37201 / 0.20 ( 8) hydrogen bonds : bond 0.03590 / 2.55 ( 885) hydrogen bonds : angle 4.28546 / 3.10 ( 2595) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8791 (tmm) cc_final: 0.8397 (tmm) REVERT: A 423 GLN cc_start: 0.8702 (tp40) cc_final: 0.8338 (tp-100) REVERT: A 644 MET cc_start: 0.7614 (ptt) cc_final: 0.7284 (ptt) REVERT: A 749 TRP cc_start: 0.4952 (OUTLIER) cc_final: 0.4711 (t-100) REVERT: C 308 MET cc_start: 0.8578 (tmm) cc_final: 0.8284 (tmm) REVERT: C 473 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: C 644 MET cc_start: 0.7690 (ptt) cc_final: 0.7365 (ptt) REVERT: D 644 MET cc_start: 0.7637 (ptt) cc_final: 0.7313 (ptt) REVERT: B 457 VAL cc_start: 0.8434 (m) cc_final: 0.8016 (t) REVERT: B 644 MET cc_start: 0.7676 (ptt) cc_final: 0.7341 (ptt) outliers start: 21 outliers final: 11 residues processed: 180 average time/residue: 0.2337 time to fit residues: 66.4369 Evaluate side-chains 172 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN C 423 GLN D 364 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.185687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141601 restraints weight = 54106.795| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.41 r_work: 0.3249 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16476 Z= 0.205 Angle : 0.510 7.525 22380 Z= 0.270 Chirality : 0.036 0.128 2524 Planarity : 0.004 0.062 2736 Dihedral : 15.609 170.803 3068 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.20 % Allowed : 10.83 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1992 helix: 1.36 (0.15), residues: 1224 sheet: -1.84 (0.56), residues: 56 loop : -1.31 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.018 0.001 TYR D 309 PHE 0.016 0.001 PHE A 473 TRP 0.008 0.001 TRP D 697 HIS 0.007 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (16472) covalent geometry : angle 0.50198 / 0.27 (22372) SS BOND : bond 0.01958 / 0.92 ( 4) SS BOND : angle 4.75041 / 2.56 ( 8) hydrogen bonds : bond 0.03694 / 2.63 ( 885) hydrogen bonds : angle 4.32408 / 3.12 ( 2595) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8746 (tmm) cc_final: 0.8360 (tmm) REVERT: A 696 ILE cc_start: 0.8236 (tp) cc_final: 0.8024 (tp) REVERT: A 749 TRP cc_start: 0.4987 (OUTLIER) cc_final: 0.4751 (t-100) REVERT: C 308 MET cc_start: 0.8562 (tmm) cc_final: 0.8244 (tmm) REVERT: C 473 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.7029 (m-80) REVERT: C 749 TRP cc_start: 0.5059 (OUTLIER) cc_final: 0.4715 (t-100) REVERT: D 423 GLN cc_start: 0.8657 (tp40) cc_final: 0.8320 (tp-100) REVERT: B 644 MET cc_start: 0.7762 (ptt) cc_final: 0.7459 (ptt) outliers start: 18 outliers final: 13 residues processed: 168 average time/residue: 0.2352 time to fit residues: 62.1594 Evaluate side-chains 168 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 749 TRP Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.186785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143036 restraints weight = 53667.545| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.42 r_work: 0.3260 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16476 Z= 0.138 Angle : 0.467 6.043 22380 Z= 0.247 Chirality : 0.034 0.130 2524 Planarity : 0.003 0.056 2736 Dihedral : 14.902 168.700 3068 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.00 % Allowed : 11.30 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.74 (0.20), residues: 1992 helix: 1.57 (0.16), residues: 1224 sheet: -1.66 (0.56), residues: 56 loop : -1.25 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 701 TYR 0.015 0.001 TYR C 309 PHE 0.015 0.001 PHE A 473 TRP 0.006 0.001 TRP C 426 HIS 0.003 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16472) covalent geometry : angle 0.46347 / 0.25 (22372) SS BOND : bond 0.01131 / 0.53 ( 4) SS BOND : angle 3.19991 / 1.71 ( 8) hydrogen bonds : bond 0.03382 / 2.41 ( 885) hydrogen bonds : angle 4.16534 / 3.00 ( 2595) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8776 (tmm) cc_final: 0.8366 (tmm) REVERT: A 696 ILE cc_start: 0.8182 (tp) cc_final: 0.7928 (tp) REVERT: A 749 TRP cc_start: 0.5032 (OUTLIER) cc_final: 0.4782 (t-100) REVERT: C 308 MET cc_start: 0.8642 (tmm) cc_final: 0.8313 (tmm) REVERT: C 644 MET cc_start: 0.7728 (ptt) cc_final: 0.7428 (ptt) REVERT: C 749 TRP cc_start: 0.5059 (OUTLIER) cc_final: 0.4726 (t-100) REVERT: D 631 TYR cc_start: 0.8060 (t80) cc_final: 0.7735 (t80) REVERT: B 644 MET cc_start: 0.7710 (ptt) cc_final: 0.7389 (ptt) outliers start: 15 outliers final: 11 residues processed: 169 average time/residue: 0.2305 time to fit residues: 61.4076 Evaluate side-chains 162 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 749 TRP Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 749 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 54 optimal weight: 0.0070 chunk 192 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN C 423 GLN D 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.187566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143988 restraints weight = 53833.147| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.40 r_work: 0.3274 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16476 Z= 0.119 Angle : 0.452 5.310 22380 Z= 0.239 Chirality : 0.033 0.156 2524 Planarity : 0.003 0.050 2736 Dihedral : 14.318 167.307 3068 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.27 % Allowed : 11.30 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.90 (0.20), residues: 1992 helix: 1.66 (0.16), residues: 1240 sheet: -1.56 (0.56), residues: 56 loop : -1.20 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 557 TYR 0.014 0.001 TYR C 309 PHE 0.013 0.001 PHE A 473 TRP 0.006 0.001 TRP C 426 HIS 0.003 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (16472) covalent geometry : angle 0.45065 / 0.24 (22372) SS BOND : bond 0.00577 / 0.27 ( 4) SS BOND : angle 1.91535 / 1.03 ( 8) hydrogen bonds : bond 0.03209 / 2.29 ( 885) hydrogen bonds : angle 4.07087 / 2.93 ( 2595) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8707 (tmm) cc_final: 0.8314 (tmm) REVERT: A 696 ILE cc_start: 0.8201 (tp) cc_final: 0.7968 (tp) REVERT: A 749 TRP cc_start: 0.5031 (OUTLIER) cc_final: 0.4775 (t-100) REVERT: C 308 MET cc_start: 0.8546 (tmm) cc_final: 0.8245 (tmm) REVERT: C 644 MET cc_start: 0.7681 (ptt) cc_final: 0.7387 (ptt) REVERT: C 749 TRP cc_start: 0.5016 (OUTLIER) cc_final: 0.4661 (t-100) REVERT: D 423 GLN cc_start: 0.8551 (tp40) cc_final: 0.8342 (tp-100) REVERT: D 631 TYR cc_start: 0.8022 (t80) cc_final: 0.7699 (t80) REVERT: D 644 MET cc_start: 0.7689 (ptt) cc_final: 0.7416 (ptt) REVERT: B 644 MET cc_start: 0.7648 (ptt) cc_final: 0.7330 (ptt) REVERT: B 684 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7368 (mp0) outliers start: 19 outliers final: 13 residues processed: 167 average time/residue: 0.2455 time to fit residues: 64.8278 Evaluate side-chains 168 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 749 TRP Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 156 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.186694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142623 restraints weight = 53803.040| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.44 r_work: 0.3266 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16476 Z= 0.146 Angle : 0.463 4.427 22380 Z= 0.245 Chirality : 0.034 0.159 2524 Planarity : 0.003 0.046 2736 Dihedral : 13.862 167.037 3068 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.20 % Allowed : 11.63 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.90 (0.20), residues: 1992 helix: 1.63 (0.16), residues: 1252 sheet: -1.58 (0.56), residues: 56 loop : -1.15 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 557 TYR 0.014 0.001 TYR C 309 PHE 0.013 0.001 PHE D 429 TRP 0.007 0.001 TRP C 426 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16472) covalent geometry : angle 0.46182 / 0.24 (22372) SS BOND : bond 0.00529 / 0.25 ( 4) SS BOND : angle 1.86805 / 1.01 ( 8) hydrogen bonds : bond 0.03226 / 2.30 ( 885) hydrogen bonds : angle 4.04661 / 2.91 ( 2595) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8836 (tmm) cc_final: 0.8363 (tmm) REVERT: A 696 ILE cc_start: 0.8182 (tp) cc_final: 0.7978 (tp) REVERT: A 749 TRP cc_start: 0.4933 (OUTLIER) cc_final: 0.4693 (t-100) REVERT: C 308 MET cc_start: 0.8705 (tmm) cc_final: 0.8327 (tmm) REVERT: C 749 TRP cc_start: 0.5020 (OUTLIER) cc_final: 0.4671 (t-100) REVERT: D 423 GLN cc_start: 0.8681 (tp40) cc_final: 0.8450 (tp-100) REVERT: D 631 TYR cc_start: 0.8036 (t80) cc_final: 0.7708 (t80) REVERT: B 684 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7145 (mp0) outliers start: 18 outliers final: 13 residues processed: 162 average time/residue: 0.2429 time to fit residues: 61.9770 Evaluate side-chains 167 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 749 TRP Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 181 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 0.0000 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.186488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142384 restraints weight = 53724.316| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.44 r_work: 0.3267 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16476 Z= 0.156 Angle : 0.465 4.428 22380 Z= 0.245 Chirality : 0.034 0.177 2524 Planarity : 0.003 0.046 2736 Dihedral : 13.486 166.914 3068 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.20 % Allowed : 12.10 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.91 (0.20), residues: 1992 helix: 1.63 (0.16), residues: 1252 sheet: -1.61 (0.56), residues: 56 loop : -1.14 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 557 TYR 0.015 0.001 TYR C 309 PHE 0.013 0.001 PHE B 429 TRP 0.007 0.001 TRP B 697 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (16472) covalent geometry : angle 0.46418 / 0.25 (22372) SS BOND : bond 0.00347 / 0.16 ( 4) SS BOND : angle 1.29483 / 0.70 ( 8) hydrogen bonds : bond 0.03221 / 2.30 ( 885) hydrogen bonds : angle 4.05254 / 2.92 ( 2595) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8835 (tmm) cc_final: 0.8356 (tmm) REVERT: A 696 ILE cc_start: 0.8175 (tp) cc_final: 0.7968 (tp) REVERT: A 749 TRP cc_start: 0.4933 (OUTLIER) cc_final: 0.4700 (t-100) REVERT: C 308 MET cc_start: 0.8721 (tmm) cc_final: 0.8334 (tmm) REVERT: C 749 TRP cc_start: 0.5018 (OUTLIER) cc_final: 0.4661 (t-100) REVERT: D 420 ARG cc_start: 0.8359 (mpp80) cc_final: 0.8108 (mtt90) REVERT: D 631 TYR cc_start: 0.8039 (t80) cc_final: 0.7714 (t80) REVERT: B 684 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: B 696 ILE cc_start: 0.8009 (tp) cc_final: 0.7783 (tp) outliers start: 18 outliers final: 13 residues processed: 161 average time/residue: 0.2472 time to fit residues: 62.5173 Evaluate side-chains 167 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 749 TRP Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 118 optimal weight: 0.0770 chunk 99 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 184 optimal weight: 1.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN C 423 GLN D 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.187977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145181 restraints weight = 53543.217| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.36 r_work: 0.3296 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16476 Z= 0.102 Angle : 0.441 4.344 22380 Z= 0.232 Chirality : 0.033 0.176 2524 Planarity : 0.003 0.046 2736 Dihedral : 12.996 165.475 3068 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.07 % Allowed : 12.30 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1992 helix: 1.84 (0.16), residues: 1240 sheet: -1.47 (0.56), residues: 56 loop : -1.09 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 557 TYR 0.014 0.001 TYR C 309 PHE 0.012 0.001 PHE B 429 TRP 0.008 0.001 TRP B 697 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (16472) covalent geometry : angle 0.43982 / 0.23 (22372) SS BOND : bond 0.00432 / 0.20 ( 4) SS BOND : angle 1.39267 / 0.75 ( 8) hydrogen bonds : bond 0.03003 / 2.14 ( 885) hydrogen bonds : angle 3.93955 / 2.83 ( 2595) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 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 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8852 (tmm) cc_final: 0.8375 (tmm) REVERT: A 696 ILE cc_start: 0.8126 (tp) cc_final: 0.7916 (tp) REVERT: A 749 TRP cc_start: 0.4920 (OUTLIER) cc_final: 0.4685 (t-100) REVERT: C 308 MET cc_start: 0.8738 (tmm) cc_final: 0.8341 (tmm) REVERT: C 749 TRP cc_start: 0.5007 (OUTLIER) cc_final: 0.4653 (t-100) REVERT: D 397 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8688 (tm-30) REVERT: D 420 ARG cc_start: 0.8353 (mpp80) cc_final: 0.8087 (mtt90) REVERT: D 631 TYR cc_start: 0.8019 (t80) cc_final: 0.7709 (t80) REVERT: B 644 MET cc_start: 0.7739 (ptt) cc_final: 0.7430 (ptt) REVERT: B 684 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7601 (mt-10) outliers start: 16 outliers final: 13 residues processed: 162 average time/residue: 0.2564 time to fit residues: 65.3631 Evaluate side-chains 169 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 749 TRP Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.186806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141816 restraints weight = 54409.861| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.50 r_work: 0.3253 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16476 Z= 0.175 Angle : 0.476 4.538 22380 Z= 0.250 Chirality : 0.035 0.164 2524 Planarity : 0.003 0.044 2736 Dihedral : 13.061 166.680 3068 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.07 % Allowed : 12.63 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.20), residues: 1992 helix: 1.68 (0.16), residues: 1252 sheet: -1.63 (0.56), residues: 56 loop : -1.11 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 557 TYR 0.014 0.001 TYR C 309 PHE 0.014 0.001 PHE B 649 TRP 0.010 0.001 TRP B 697 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (16472) covalent geometry : angle 0.47560 / 0.25 (22372) SS BOND : bond 0.00402 / 0.19 ( 4) SS BOND : angle 1.29921 / 0.70 ( 8) hydrogen bonds : bond 0.03203 / 2.28 ( 885) hydrogen bonds : angle 4.03544 / 2.91 ( 2595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5604.77 seconds wall clock time: 96 minutes 1.58 seconds (5761.58 seconds total)