Starting phenix.real_space_refine on Fri Mar 6 17:44:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rqy_24640/03_2026/7rqy_24640_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rqy_24640/03_2026/7rqy_24640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rqy_24640/03_2026/7rqy_24640_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rqy_24640/03_2026/7rqy_24640_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rqy_24640/03_2026/7rqy_24640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rqy_24640/03_2026/7rqy_24640.map" } resolution = 3.04 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= 0.011 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 80 5.16 5 C 11016 2.51 5 N 2620 2.21 5 O 2940 1.98 5 H 15388 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32052 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7877 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 8, 'ASP:plan': 10, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "B" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7877 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 8, 'ASP:plan': 10, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "C" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7877 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 8, 'ASP:plan': 10, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "D" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7877 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 8, 'ASP:plan': 10, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 136 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 168 Unusual residues: {'6EU': 1, '6OU': 3, 'LBN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 136 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'6OU:plan-1': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 104 Unusual residues: {'6EU': 1, '6OU': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA A 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA B 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA D 204 " occ=0.50 Time building chain proxies: 6.41, per 1000 atoms: 0.20 Number of scatterers: 32052 At special positions: 0 Unit cell: (124.509, 123.48, 109.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 8 15.00 O 2940 8.00 N 2620 7.00 C 11016 6.00 H 15388 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=2.07 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.07 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.07 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.07 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: 2.62 Conformation dependent library (CDL) restraints added in 895.4 milliseconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 66.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.716A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.609A pdb=" N LYS A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 366 removed outlier: 4.096A pdb=" N LEU A 365 " --> pdb=" O CYS A 362 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 366 " --> pdb=" O ARG A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.597A pdb=" N ILE A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 4.019A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.501A pdb=" N TYR A 435 " --> pdb=" O LYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 removed outlier: 3.609A pdb=" N PHE A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) 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: 3.770A pdb=" N ASP A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.599A 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 510 through 531 removed outlier: 3.583A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 520 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.692A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 removed outlier: 3.687A pdb=" N THR A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 559 " --> pdb=" O THR A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 removed outlier: 3.901A pdb=" N VAL A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 599 removed outlier: 3.607A pdb=" N VAL A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.690A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.574A pdb=" N ILE A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 691 removed outlier: 3.527A pdb=" N LEU A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.639A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 4.290A pdb=" N PHE A 720 " --> pdb=" O MET A 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.716A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.609A pdb=" N LYS B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 362 through 366 removed outlier: 4.096A pdb=" N LEU B 365 " --> pdb=" O CYS B 362 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER B 366 " --> pdb=" O ARG B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 366' Processing helix chain 'B' and resid 394 through 401 removed outlier: 3.597A pdb=" N ILE B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 removed outlier: 4.018A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 removed outlier: 3.609A pdb=" N PHE B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) 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: 3.770A pdb=" N ASP B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 3.598A 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 510 through 531 removed outlier: 3.584A pdb=" N LEU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 520 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.691A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.688A pdb=" N THR B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 559 " --> pdb=" O THR B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.900A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 599 removed outlier: 3.607A pdb=" N VAL B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 599 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.690A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.574A pdb=" N ILE B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 691 removed outlier: 3.527A pdb=" N LEU B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 removed outlier: 3.639A pdb=" N LEU B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 720 removed outlier: 4.290A pdb=" N PHE B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.715A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.609A pdb=" N LYS C 303 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 362 through 366 removed outlier: 4.096A pdb=" N LEU C 365 " --> pdb=" O CYS C 362 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER C 366 " --> pdb=" O ARG C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 362 through 366' Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.597A pdb=" N ILE C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 removed outlier: 4.019A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.501A pdb=" N TYR C 435 " --> pdb=" O LYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 removed outlier: 3.609A pdb=" N PHE C 489 " --> pdb=" O GLY C 485 " (cutoff:3.500A) 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: 3.770A pdb=" N ASP C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 3.598A 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 510 through 531 removed outlier: 3.583A pdb=" N LEU C 515 " --> pdb=" O TYR C 511 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 520 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.692A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 559 removed outlier: 3.688A pdb=" N THR C 556 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 559 " --> pdb=" O THR C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 575 removed outlier: 3.901A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 599 removed outlier: 3.606A pdb=" N VAL C 586 " --> pdb=" O PHE C 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 599 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.690A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.574A pdb=" N ILE C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 691 removed outlier: 3.527A pdb=" N LEU C 678 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 712 removed outlier: 3.640A pdb=" N LEU C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C 712 " --> pdb=" O THR C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 720 removed outlier: 4.289A pdb=" N PHE C 720 " --> pdb=" O MET C 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.715A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.608A pdb=" N LYS D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 362 through 366 removed outlier: 4.096A pdb=" N LEU D 365 " --> pdb=" O CYS D 362 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER D 366 " --> pdb=" O ARG D 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 362 through 366' Processing helix chain 'D' and resid 394 through 401 removed outlier: 3.597A pdb=" N ILE D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 removed outlier: 4.018A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.501A pdb=" N TYR D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 removed outlier: 3.608A pdb=" N PHE D 489 " --> pdb=" O GLY D 485 " (cutoff:3.500A) 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: 3.771A pdb=" N ASP D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) removed outlier: 3.600A 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 510 through 531 removed outlier: 3.584A pdb=" N LEU D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE D 516 " --> pdb=" O SER D 512 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 520 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.691A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 559 removed outlier: 3.688A pdb=" N THR D 556 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 559 " --> pdb=" O THR D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 575 removed outlier: 3.902A pdb=" N VAL D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 599 removed outlier: 3.607A pdb=" N VAL D 586 " --> pdb=" O PHE D 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 599 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.691A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.574A pdb=" N ILE D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 691 removed outlier: 3.527A pdb=" N LEU D 678 " --> pdb=" O LEU D 674 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 712 removed outlier: 3.640A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 720 removed outlier: 4.291A pdb=" N PHE D 720 " --> pdb=" O MET D 716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.639A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 377 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 728 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.639A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 377 " --> pdb=" O TYR B 374 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 728 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.638A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 377 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL C 728 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 372 through 374 removed outlier: 3.639A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 377 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL D 728 " --> pdb=" O ASP D 737 " (cutoff:3.500A) 913 hydrogen bonds defined for protein. 2715 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: 8.10 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15368 1.04 - 1.23: 601 1.23 - 1.43: 6749 1.43 - 1.63: 9570 1.63 - 1.83: 160 Bond restraints: 32448 Sorted by residual: bond pdb=" CAS 6EU A 901 " pdb=" CAX 6EU A 901 " ideal model delta sigma weight residual 1.334 1.606 -0.272 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAS 6EU D 901 " pdb=" CAX 6EU D 901 " ideal model delta sigma weight residual 1.334 1.605 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAS 6EU B 901 " pdb=" CAX 6EU B 901 " ideal model delta sigma weight residual 1.334 1.605 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAS 6EU C 902 " pdb=" CAX 6EU C 902 " ideal model delta sigma weight residual 1.334 1.605 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAW 6EU C 902 " pdb=" CBA 6EU C 902 " ideal model delta sigma weight residual 1.339 1.519 -0.180 2.00e-02 2.50e+03 8.10e+01 ... (remaining 32443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 57591 3.17 - 6.33: 353 6.33 - 9.50: 44 9.50 - 12.66: 20 12.66 - 15.83: 8 Bond angle restraints: 58016 Sorted by residual: angle pdb=" N GLU B 391 " pdb=" CA GLU B 391 " pdb=" C GLU B 391 " ideal model delta sigma weight residual 111.02 118.42 -7.40 1.22e+00 6.72e-01 3.68e+01 angle pdb=" N GLU C 391 " pdb=" CA GLU C 391 " pdb=" C GLU C 391 " ideal model delta sigma weight residual 111.02 118.40 -7.38 1.22e+00 6.72e-01 3.66e+01 angle pdb=" N GLU A 391 " pdb=" CA GLU A 391 " pdb=" C GLU A 391 " ideal model delta sigma weight residual 111.02 118.37 -7.35 1.22e+00 6.72e-01 3.63e+01 angle pdb=" N GLU D 391 " pdb=" CA GLU D 391 " pdb=" C GLU D 391 " ideal model delta sigma weight residual 111.02 118.36 -7.34 1.22e+00 6.72e-01 3.62e+01 angle pdb=" CAM 6EU B 901 " pdb=" CAV 6EU B 901 " pdb=" CBD 6EU B 901 " ideal model delta sigma weight residual 115.62 99.79 15.83 3.00e+00 1.11e-01 2.78e+01 ... (remaining 58011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.05: 15356 33.05 - 66.11: 500 66.11 - 99.16: 44 99.16 - 132.21: 12 132.21 - 165.27: 8 Dihedral angle restraints: 15920 sinusoidal: 8304 harmonic: 7616 Sorted by residual: dihedral pdb=" C1 LBN B 902 " pdb=" O1 LBN B 902 " pdb=" P1 LBN B 902 " pdb=" O3 LBN B 902 " ideal model delta sinusoidal sigma weight residual -84.60 80.67 -165.27 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C1 LBN A 902 " pdb=" O1 LBN A 902 " pdb=" P1 LBN A 902 " pdb=" O3 LBN A 902 " ideal model delta sinusoidal sigma weight residual -84.60 80.64 -165.24 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C1 LBN C 903 " pdb=" O1 LBN C 903 " pdb=" P1 LBN C 903 " pdb=" O3 LBN C 903 " ideal model delta sinusoidal sigma weight residual -84.60 80.62 -165.22 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 15917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2563 0.089 - 0.178: 53 0.178 - 0.267: 12 0.267 - 0.357: 14 0.357 - 0.446: 14 Chirality restraints: 2656 Sorted by residual: chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.68 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.68 0.44 2.00e-01 2.50e+01 4.93e+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 -2.81 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 2653 not shown) Planarity restraints: 4880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 687 " 0.158 2.00e-02 2.50e+03 1.57e-01 3.69e+02 pdb=" CG ASN B 687 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 687 " -0.150 2.00e-02 2.50e+03 pdb=" ND2 ASN B 687 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 687 " -0.221 2.00e-02 2.50e+03 pdb="HD22 ASN B 687 " 0.226 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 687 " -0.157 2.00e-02 2.50e+03 1.57e-01 3.69e+02 pdb=" CG ASN D 687 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN D 687 " 0.150 2.00e-02 2.50e+03 pdb=" ND2 ASN D 687 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 687 " 0.221 2.00e-02 2.50e+03 pdb="HD22 ASN D 687 " -0.226 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 687 " 0.158 2.00e-02 2.50e+03 1.57e-01 3.69e+02 pdb=" CG ASN C 687 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 687 " -0.150 2.00e-02 2.50e+03 pdb=" ND2 ASN C 687 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 687 " -0.221 2.00e-02 2.50e+03 pdb="HD22 ASN C 687 " 0.226 2.00e-02 2.50e+03 ... (remaining 4877 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1849 2.20 - 2.80: 63275 2.80 - 3.40: 86163 3.40 - 4.00: 111679 4.00 - 4.60: 173355 Nonbonded interactions: 436321 Sorted by model distance: nonbonded pdb=" O ILE B 209 " pdb="HE22 GLN B 260 " model vdw 1.600 2.450 nonbonded pdb=" O ILE C 209 " pdb="HE22 GLN C 260 " model vdw 1.600 2.450 nonbonded pdb=" O ILE A 209 " pdb="HE22 GLN A 260 " model vdw 1.600 2.450 nonbonded pdb=" O ILE D 209 " pdb="HE22 GLN D 260 " model vdw 1.601 2.450 nonbonded pdb=" OD1 ASP B 296 " pdb=" HG1 THR B 298 " model vdw 1.621 2.450 ... (remaining 436316 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 197 through 752) selection = (chain 'B' and resid 197 through 752) selection = (chain 'C' and resid 197 through 752) selection = (chain 'D' and resid 197 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: 1.130 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: 0.430 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.680 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.272 17064 Z= 0.533 Angle : 0.943 15.830 23212 Z= 0.431 Chirality : 0.054 0.446 2656 Planarity : 0.004 0.055 2844 Dihedral : 17.875 165.267 6260 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -0.70 (0.18), residues: 2076 helix: 0.13 (0.15), residues: 1288 sheet: -4.09 (0.44), residues: 56 loop : -1.06 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 428 TYR 0.010 0.001 TYR C 309 PHE 0.013 0.001 PHE D 448 TRP 0.006 0.001 TRP D 372 HIS 0.002 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.01059 (17060) covalent geometry : angle 0.94201 (23204) SS BOND : bond 0.03920 ( 4) SS BOND : angle 2.05012 ( 8) hydrogen bonds : bond 0.20761 ( 913) hydrogen bonds : angle 7.39452 ( 2715) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 561 GLN cc_start: 0.8034 (mp10) cc_final: 0.7426 (pm20) REVERT: A 677 MET cc_start: 0.8428 (ttp) cc_final: 0.8028 (ttm) REVERT: B 552 MET cc_start: 0.8883 (mtt) cc_final: 0.8452 (mtt) REVERT: B 677 MET cc_start: 0.8374 (ttp) cc_final: 0.8057 (ttm) REVERT: C 552 MET cc_start: 0.8818 (mtt) cc_final: 0.8434 (mtt) REVERT: C 677 MET cc_start: 0.8330 (ttp) cc_final: 0.7935 (ttm) REVERT: C 703 ILE cc_start: 0.8639 (mt) cc_final: 0.8376 (mt) REVERT: D 592 SER cc_start: 0.8910 (t) cc_final: 0.8471 (m) REVERT: D 677 MET cc_start: 0.8404 (ttp) cc_final: 0.8083 (ttm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2397 time to fit residues: 77.0084 Evaluate side-chains 164 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 676 ASN A 687 ASN B 498 GLN B 676 ASN B 687 ASN C 378 HIS C 498 GLN C 676 ASN C 687 ASN D 378 HIS D 676 ASN D 687 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.219759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.187781 restraints weight = 47033.830| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.41 r_work: 0.3534 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17064 Z= 0.181 Angle : 0.589 7.426 23212 Z= 0.305 Chirality : 0.035 0.143 2656 Planarity : 0.004 0.053 2844 Dihedral : 16.202 164.402 2952 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.38 % Allowed : 7.27 % Favored : 92.36 % 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: -0.21 (0.18), residues: 2076 helix: 0.57 (0.15), residues: 1296 sheet: -4.19 (0.39), residues: 56 loop : -0.98 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 432 TYR 0.014 0.001 TYR D 309 PHE 0.011 0.001 PHE B 448 TRP 0.007 0.001 TRP C 549 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00403 (17060) covalent geometry : angle 0.58854 (23204) SS BOND : bond 0.00752 ( 4) SS BOND : angle 0.59759 ( 8) hydrogen bonds : bond 0.05082 ( 913) hydrogen bonds : angle 4.84394 ( 2715) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 MET cc_start: 0.8812 (ttp) cc_final: 0.8400 (ttm) REVERT: B 677 MET cc_start: 0.8727 (ttp) cc_final: 0.8364 (ttm) REVERT: C 677 MET cc_start: 0.8645 (ttp) cc_final: 0.8232 (ttm) REVERT: D 311 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6983 (tt0) REVERT: D 677 MET cc_start: 0.8787 (ttp) cc_final: 0.8386 (ttm) outliers start: 6 outliers final: 4 residues processed: 179 average time/residue: 0.2398 time to fit residues: 67.3555 Evaluate side-chains 173 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 169 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 50 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.219854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162515 restraints weight = 47100.349| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.45 r_work: 0.3438 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17064 Z= 0.128 Angle : 0.505 5.560 23212 Z= 0.265 Chirality : 0.033 0.128 2656 Planarity : 0.004 0.061 2844 Dihedral : 14.810 171.321 2952 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.44 % Allowed : 8.27 % Favored : 91.29 % 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 (0.18), residues: 2076 helix: 1.05 (0.15), residues: 1296 sheet: -4.02 (0.39), residues: 56 loop : -0.97 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 432 TYR 0.014 0.001 TYR B 309 PHE 0.009 0.001 PHE B 448 TRP 0.006 0.001 TRP C 697 HIS 0.016 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00280 (17060) covalent geometry : angle 0.50457 (23204) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.81377 ( 8) hydrogen bonds : bond 0.04320 ( 913) hydrogen bonds : angle 4.40458 ( 2715) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 MET cc_start: 0.8794 (ttp) cc_final: 0.8391 (ttm) REVERT: B 677 MET cc_start: 0.8744 (ttp) cc_final: 0.8353 (ttm) REVERT: C 378 HIS cc_start: 0.7309 (m90) cc_final: 0.6916 (m90) REVERT: C 561 GLN cc_start: 0.7863 (mp10) cc_final: 0.7110 (pm20) REVERT: C 677 MET cc_start: 0.8707 (ttp) cc_final: 0.8271 (ttm) REVERT: D 304 PHE cc_start: 0.7799 (t80) cc_final: 0.7225 (t80) REVERT: D 311 GLU cc_start: 0.7245 (mm-30) cc_final: 0.7023 (tt0) REVERT: D 677 MET cc_start: 0.8783 (ttp) cc_final: 0.8386 (ttm) outliers start: 7 outliers final: 6 residues processed: 177 average time/residue: 0.2355 time to fit residues: 66.5333 Evaluate side-chains 169 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 50.0000 chunk 44 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 HIS C 498 GLN D 410 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.220577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.172427 restraints weight = 47065.681| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.36 r_work: 0.3485 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17064 Z= 0.139 Angle : 0.496 6.341 23212 Z= 0.259 Chirality : 0.033 0.132 2656 Planarity : 0.003 0.061 2844 Dihedral : 14.146 173.655 2952 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.50 % Allowed : 9.59 % Favored : 89.91 % 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: 0.54 (0.18), residues: 2076 helix: 1.31 (0.15), residues: 1300 sheet: -3.66 (0.41), residues: 56 loop : -1.04 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 575 TYR 0.009 0.001 TYR B 309 PHE 0.009 0.001 PHE A 448 TRP 0.007 0.001 TRP C 372 HIS 0.014 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00313 (17060) covalent geometry : angle 0.49508 (23204) SS BOND : bond 0.00298 ( 4) SS BOND : angle 1.28498 ( 8) hydrogen bonds : bond 0.03698 ( 913) hydrogen bonds : angle 4.16175 ( 2715) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 169 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 378 HIS cc_start: 0.7015 (OUTLIER) cc_final: 0.6287 (p90) REVERT: B 561 GLN cc_start: 0.7937 (mp10) cc_final: 0.7234 (pm20) REVERT: B 677 MET cc_start: 0.8820 (ttp) cc_final: 0.8445 (ttm) REVERT: C 378 HIS cc_start: 0.7468 (m90) cc_final: 0.7144 (m90) REVERT: C 561 GLN cc_start: 0.7921 (mp10) cc_final: 0.7088 (pm20) REVERT: C 677 MET cc_start: 0.8800 (ttp) cc_final: 0.8364 (ttm) REVERT: D 311 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6991 (tt0) REVERT: D 677 MET cc_start: 0.8815 (ttp) cc_final: 0.8431 (ttm) outliers start: 8 outliers final: 4 residues processed: 175 average time/residue: 0.2227 time to fit residues: 62.8492 Evaluate side-chains 170 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 165 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain D residue 378 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 50.0000 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 29 optimal weight: 0.0870 chunk 185 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.220768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.172892 restraints weight = 47320.121| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.37 r_work: 0.3491 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17064 Z= 0.125 Angle : 0.475 5.813 23212 Z= 0.247 Chirality : 0.033 0.126 2656 Planarity : 0.003 0.048 2844 Dihedral : 13.998 177.067 2952 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.88 % Allowed : 9.84 % Favored : 89.29 % 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: 0.77 (0.18), residues: 2076 helix: 1.55 (0.15), residues: 1296 sheet: -3.43 (0.43), residues: 56 loop : -1.06 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 575 TYR 0.009 0.001 TYR A 351 PHE 0.009 0.001 PHE A 448 TRP 0.004 0.001 TRP A 549 HIS 0.010 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00278 (17060) covalent geometry : angle 0.47456 (23204) SS BOND : bond 0.01022 ( 4) SS BOND : angle 0.88735 ( 8) hydrogen bonds : bond 0.03517 ( 913) hydrogen bonds : angle 3.98125 ( 2715) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8079 (tt) cc_final: 0.7844 (tp) REVERT: B 561 GLN cc_start: 0.8001 (mp10) cc_final: 0.7279 (pm20) REVERT: B 677 MET cc_start: 0.8822 (ttp) cc_final: 0.8457 (ttm) REVERT: C 561 GLN cc_start: 0.7999 (mp10) cc_final: 0.7156 (pm20) REVERT: C 677 MET cc_start: 0.8797 (ttp) cc_final: 0.8369 (ttm) REVERT: D 503 LEU cc_start: 0.7953 (mt) cc_final: 0.7619 (tp) REVERT: D 677 MET cc_start: 0.8838 (ttp) cc_final: 0.8476 (ttm) outliers start: 14 outliers final: 6 residues processed: 173 average time/residue: 0.2190 time to fit residues: 62.6674 Evaluate side-chains 165 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain D residue 378 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 0.0370 chunk 138 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 134 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.220171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3928 r_free = 0.3928 target = 0.169749 restraints weight = 47036.103| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.37 r_work: 0.3455 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17064 Z= 0.127 Angle : 0.472 5.838 23212 Z= 0.245 Chirality : 0.033 0.129 2656 Planarity : 0.003 0.049 2844 Dihedral : 13.998 178.669 2952 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.69 % Allowed : 9.90 % Favored : 89.41 % 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 (0.18), residues: 2076 helix: 1.68 (0.15), residues: 1296 sheet: -3.30 (0.45), residues: 56 loop : -1.08 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 409 TYR 0.008 0.001 TYR B 309 PHE 0.008 0.001 PHE D 448 TRP 0.005 0.001 TRP C 740 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00288 (17060) covalent geometry : angle 0.47170 (23204) SS BOND : bond 0.00565 ( 4) SS BOND : angle 1.16199 ( 8) hydrogen bonds : bond 0.03388 ( 913) hydrogen bonds : angle 3.92456 ( 2715) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8049 (tt) cc_final: 0.7825 (tp) REVERT: C 561 GLN cc_start: 0.7952 (mp10) cc_final: 0.7174 (pm20) REVERT: C 677 MET cc_start: 0.8795 (ttp) cc_final: 0.8425 (ttm) REVERT: D 503 LEU cc_start: 0.7962 (mt) cc_final: 0.7625 (tp) outliers start: 11 outliers final: 7 residues processed: 173 average time/residue: 0.2182 time to fit residues: 62.2854 Evaluate side-chains 170 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 129 optimal weight: 0.2980 chunk 64 optimal weight: 6.9990 chunk 205 optimal weight: 20.0000 chunk 189 optimal weight: 2.9990 chunk 52 optimal weight: 40.0000 chunk 60 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.216828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.168206 restraints weight = 47405.869| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.35 r_work: 0.3415 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17064 Z= 0.272 Angle : 0.586 8.561 23212 Z= 0.297 Chirality : 0.039 0.152 2656 Planarity : 0.004 0.045 2844 Dihedral : 14.687 177.538 2952 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.69 % Allowed : 10.09 % Favored : 89.22 % 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: 0.48 (0.18), residues: 2076 helix: 1.26 (0.14), residues: 1292 sheet: -3.46 (0.44), residues: 56 loop : -1.04 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 579 TYR 0.011 0.002 TYR C 530 PHE 0.015 0.002 PHE D 448 TRP 0.005 0.001 TRP C 549 HIS 0.006 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00632 (17060) covalent geometry : angle 0.58554 (23204) SS BOND : bond 0.00294 ( 4) SS BOND : angle 1.28736 ( 8) hydrogen bonds : bond 0.04314 ( 913) hydrogen bonds : angle 4.21800 ( 2715) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 339 LEU cc_start: 0.8042 (tt) cc_final: 0.7809 (tp) REVERT: B 369 PHE cc_start: 0.7810 (m-10) cc_final: 0.7548 (m-10) REVERT: B 498 GLN cc_start: 0.8289 (mt0) cc_final: 0.8055 (mt0) REVERT: C 259 ASN cc_start: 0.5535 (t0) cc_final: 0.5095 (m-40) REVERT: C 677 MET cc_start: 0.8898 (ttp) cc_final: 0.8645 (ttm) REVERT: D 503 LEU cc_start: 0.7931 (mt) cc_final: 0.7562 (tp) outliers start: 11 outliers final: 10 residues processed: 177 average time/residue: 0.2309 time to fit residues: 65.9000 Evaluate side-chains 178 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.218667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.168607 restraints weight = 47218.434| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.40 r_work: 0.3353 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17064 Z= 0.141 Angle : 0.494 6.709 23212 Z= 0.255 Chirality : 0.033 0.118 2656 Planarity : 0.003 0.045 2844 Dihedral : 14.143 177.282 2952 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.50 % Allowed : 10.59 % Favored : 88.91 % 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: 0.72 (0.18), residues: 2076 helix: 1.52 (0.15), residues: 1300 sheet: -3.28 (0.46), residues: 56 loop : -1.12 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 409 TYR 0.013 0.001 TYR A 309 PHE 0.009 0.001 PHE D 448 TRP 0.006 0.001 TRP C 549 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00323 (17060) covalent geometry : angle 0.49403 (23204) SS BOND : bond 0.00286 ( 4) SS BOND : angle 1.06482 ( 8) hydrogen bonds : bond 0.03497 ( 913) hydrogen bonds : angle 3.98421 ( 2715) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: B 369 PHE cc_start: 0.7618 (m-10) cc_final: 0.7301 (m-10) REVERT: B 424 ASP cc_start: 0.7651 (t0) cc_final: 0.7396 (t0) REVERT: C 259 ASN cc_start: 0.5517 (t0) cc_final: 0.5079 (m-40) REVERT: D 503 LEU cc_start: 0.7897 (mt) cc_final: 0.7548 (tp) outliers start: 8 outliers final: 7 residues processed: 174 average time/residue: 0.2426 time to fit residues: 66.7486 Evaluate side-chains 172 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 59 optimal weight: 30.0000 chunk 193 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.219859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3933 r_free = 0.3933 target = 0.170233 restraints weight = 47085.621| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.37 r_work: 0.3464 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17064 Z= 0.112 Angle : 0.460 5.449 23212 Z= 0.239 Chirality : 0.033 0.120 2656 Planarity : 0.003 0.045 2844 Dihedral : 13.618 177.505 2952 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.63 % Allowed : 10.46 % Favored : 88.91 % 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: 1.06 (0.18), residues: 2076 helix: 1.80 (0.15), residues: 1296 sheet: -3.25 (0.47), residues: 56 loop : -1.00 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 409 TYR 0.008 0.001 TYR B 309 PHE 0.007 0.001 PHE C 304 TRP 0.007 0.001 TRP C 549 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00254 (17060) covalent geometry : angle 0.45934 (23204) SS BOND : bond 0.00229 ( 4) SS BOND : angle 0.93170 ( 8) hydrogen bonds : bond 0.03162 ( 913) hydrogen bonds : angle 3.81181 ( 2715) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: C 259 ASN cc_start: 0.5474 (t0) cc_final: 0.4927 (m-40) REVERT: D 424 ASP cc_start: 0.7779 (t0) cc_final: 0.7494 (t0) REVERT: D 503 LEU cc_start: 0.7900 (mt) cc_final: 0.7536 (tp) REVERT: D 523 MET cc_start: 0.7951 (ttp) cc_final: 0.7538 (ttp) outliers start: 10 outliers final: 6 residues processed: 175 average time/residue: 0.2407 time to fit residues: 66.7433 Evaluate side-chains 171 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 17 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.219215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.170420 restraints weight = 47409.063| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.40 r_work: 0.3443 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17064 Z= 0.147 Angle : 0.483 6.531 23212 Z= 0.250 Chirality : 0.034 0.118 2656 Planarity : 0.003 0.046 2844 Dihedral : 13.767 177.684 2952 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.50 % Allowed : 10.71 % Favored : 88.78 % 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: 1.02 (0.18), residues: 2076 helix: 1.77 (0.15), residues: 1296 sheet: -3.25 (0.47), residues: 56 loop : -1.02 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 409 TYR 0.009 0.001 TYR A 530 PHE 0.012 0.001 PHE C 304 TRP 0.004 0.001 TRP D 372 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00339 (17060) covalent geometry : angle 0.48311 (23204) SS BOND : bond 0.00271 ( 4) SS BOND : angle 0.84443 ( 8) hydrogen bonds : bond 0.03361 ( 913) hydrogen bonds : angle 3.85703 ( 2715) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: B 369 PHE cc_start: 0.7694 (m-10) cc_final: 0.7453 (m-10) REVERT: B 424 ASP cc_start: 0.7738 (t0) cc_final: 0.7427 (t0) REVERT: C 259 ASN cc_start: 0.5596 (t0) cc_final: 0.5089 (m-40) REVERT: D 424 ASP cc_start: 0.7795 (t0) cc_final: 0.7489 (t0) REVERT: D 503 LEU cc_start: 0.7904 (mt) cc_final: 0.7530 (tp) REVERT: D 523 MET cc_start: 0.7955 (ttp) cc_final: 0.7528 (ttp) outliers start: 8 outliers final: 7 residues processed: 177 average time/residue: 0.2296 time to fit residues: 65.1572 Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 105 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 94 optimal weight: 0.0040 chunk 194 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.220195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171121 restraints weight = 47323.739| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.37 r_work: 0.3455 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17064 Z= 0.116 Angle : 0.460 5.741 23212 Z= 0.238 Chirality : 0.033 0.119 2656 Planarity : 0.003 0.046 2844 Dihedral : 13.567 177.194 2952 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.31 % Allowed : 10.78 % Favored : 88.91 % 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: 1.16 (0.18), residues: 2076 helix: 1.90 (0.15), residues: 1296 sheet: -3.22 (0.47), residues: 56 loop : -1.00 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 428 TYR 0.008 0.001 TYR B 309 PHE 0.011 0.001 PHE C 304 TRP 0.006 0.001 TRP C 549 HIS 0.007 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00262 (17060) covalent geometry : angle 0.45957 (23204) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.82080 ( 8) hydrogen bonds : bond 0.03132 ( 913) hydrogen bonds : angle 3.75834 ( 2715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8259.04 seconds wall clock time: 140 minutes 23.73 seconds (8423.73 seconds total)