Starting phenix.real_space_refine on Tue Sep 15 03:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bpa_30149/09_2026/7bpa_30149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bpa_30149/09_2026/7bpa_30149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bpa_30149/09_2026/7bpa_30149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bpa_30149/09_2026/7bpa_30149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bpa_30149/09_2026/7bpa_30149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bpa_30149/09_2026/7bpa_30149.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bpa_30149/09_2026/7bpa_30149.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bpa_30149/09_2026/7bpa_30149.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 180 5.16 5 C 22086 2.51 5 N 6282 2.21 5 O 6792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35370 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "B" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "C" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "D" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "E" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "F" Number of atoms: 5837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 742, 5829 Classifications: {'peptide': 742} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5913 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AASP A 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 592 " occ=0.50 residue: pdb=" N AASP B 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 592 " occ=0.50 residue: pdb=" N AASP C 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 592 " occ=0.50 residue: pdb=" N AASP D 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP D 592 " occ=0.50 residue: pdb=" N AASP E 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP E 592 " occ=0.50 residue: pdb=" N AASP F 592 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP F 592 " occ=0.50 Time building chain proxies: 13.87, per 1000 atoms: 0.39 Number of scatterers: 35370 At special positions: 0 Unit cell: (172.753, 183.483, 100.862, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 30 15.00 O 6792 8.00 N 6282 7.00 C 22086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 2.8 seconds 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8340 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 30 sheets defined 47.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 130 through 139 removed outlier: 4.817A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.612A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.741A pdb=" N LEU A 213 " --> pdb=" O CYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.578A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.828A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 278 through 296 removed outlier: 3.815A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.675A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.557A pdb=" N SER A 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 353' Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.800A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.712A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.619A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 495 removed outlier: 3.951A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 506 removed outlier: 4.624A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.633A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.874A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.565A pdb=" N ASN A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 662 removed outlier: 3.964A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.924A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 713 removed outlier: 3.685A pdb=" N THR A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A 692 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.555A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.633A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 130 through 139 removed outlier: 4.862A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.614A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.749A pdb=" N LEU B 213 " --> pdb=" O CYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.612A pdb=" N LEU B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.849A pdb=" N ILE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 278 through 296 removed outlier: 3.760A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.682A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.542A pdb=" N SER B 352 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 353' Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.783A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.737A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 444 Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.583A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 495 removed outlier: 3.950A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.621A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.658A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.910A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.519A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 662 removed outlier: 3.972A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.908A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 713 removed outlier: 3.668A pdb=" N THR B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.567A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 removed outlier: 3.662A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 130 through 139 removed outlier: 4.849A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.662A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.717A pdb=" N LEU C 213 " --> pdb=" O CYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.590A pdb=" N LEU C 224 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.842A pdb=" N ILE C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 278 through 296 removed outlier: 3.795A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.647A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.542A pdb=" N SER C 352 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 402 removed outlier: 3.777A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.748A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 444 Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.615A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 495 removed outlier: 3.937A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 removed outlier: 4.617A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.614A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.879A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.547A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 649 through 662 removed outlier: 3.973A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.904A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 713 removed outlier: 3.767A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN C 692 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.556A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 removed outlier: 3.642A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 130 through 139 removed outlier: 4.819A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.611A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 removed outlier: 3.742A pdb=" N LEU D 213 " --> pdb=" O CYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.579A pdb=" N LEU D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.828A pdb=" N ILE D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 278 through 296 removed outlier: 3.816A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.671A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.554A pdb=" N SER D 352 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 349 through 353' Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 402 removed outlier: 3.801A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.718A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.603A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 495 removed outlier: 3.950A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 506 removed outlier: 4.622A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.634A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.875A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 557 No H-bonds generated for 'chain 'D' and resid 555 through 557' Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.568A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 662 removed outlier: 3.963A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.908A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 713 removed outlier: 3.682A pdb=" N THR D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU D 689 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 741 removed outlier: 3.549A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 removed outlier: 3.632A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 139 removed outlier: 4.863A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.615A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 220 Processing helix chain 'E' and resid 220 through 226 removed outlier: 3.610A pdb=" N LEU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.852A pdb=" N ILE E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 278 through 296 removed outlier: 3.787A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.685A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.544A pdb=" N SER E 352 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 402 removed outlier: 3.780A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.734A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 444 Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.582A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 495 removed outlier: 3.948A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.625A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.658A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.895A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 557 No H-bonds generated for 'chain 'E' and resid 555 through 557' Processing helix chain 'E' and resid 558 through 569 Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.517A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 662 removed outlier: 3.973A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.910A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 713 removed outlier: 3.668A pdb=" N THR E 688 " --> pdb=" O GLY E 684 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU E 689 " --> pdb=" O ALA E 685 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 741 removed outlier: 3.562A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 removed outlier: 3.661A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 130 through 139 removed outlier: 4.854A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.660A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 removed outlier: 3.715A pdb=" N LEU F 213 " --> pdb=" O CYS F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 226 removed outlier: 3.590A pdb=" N LEU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 250 through 262 removed outlier: 3.843A pdb=" N ILE F 254 " --> pdb=" O GLY F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 278 through 296 removed outlier: 3.794A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.647A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.546A pdb=" N SER F 352 " --> pdb=" O ARG F 349 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 349 through 353' Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 402 removed outlier: 3.779A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.748A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 444 Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.612A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 495 removed outlier: 3.501A pdb=" N LYS F 486 " --> pdb=" O LEU F 482 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 506 removed outlier: 4.614A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.613A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.879A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 557 No H-bonds generated for 'chain 'F' and resid 555 through 557' Processing helix chain 'F' and resid 558 through 569 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 removed outlier: 3.544A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 649 through 662 removed outlier: 3.987A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.884A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 713 removed outlier: 3.766A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN F 692 " --> pdb=" O THR F 688 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG F 713 " --> pdb=" O ARG F 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 741 removed outlier: 3.554A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 removed outlier: 3.640A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 removed outlier: 5.983A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS A 81 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER A 42 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.802A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.846A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.658A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.755A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 29 removed outlier: 6.003A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LYS B 81 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER B 42 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 26 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.791A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 147 removed outlier: 3.856A pdb=" N ARG B 144 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.673A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.755A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 26 through 29 removed outlier: 5.991A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 26 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.814A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 114 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.850A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.649A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.725A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 26 through 29 removed outlier: 5.984A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N LYS D 81 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N SER D 42 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 26 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.805A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 144 through 147 removed outlier: 3.844A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.659A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.755A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 26 through 29 removed outlier: 6.003A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS E 81 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER E 42 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E 26 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 151 through 156 removed outlier: 6.792A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.857A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.667A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.750A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 26 through 29 removed outlier: 5.991A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LYS F 81 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER F 42 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU F 26 " --> pdb=" O ILE F 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.815A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 144 through 147 removed outlier: 3.849A pdb=" N ARG F 144 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.650A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.725A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1385 hydrogen bonds defined for protein. 3951 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: 8.36 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11109 1.34 - 1.46: 5871 1.46 - 1.58: 18636 1.58 - 1.70: 54 1.70 - 1.82: 288 Bond restraints: 35958 Sorted by residual: bond pdb=" O3A ANP D 901 " pdb=" PB ANP D 901 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" O3A ANP A 902 " pdb=" PB ANP A 902 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O3A ANP E 901 " pdb=" PB ANP E 901 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.41e+01 bond pdb=" O3A ANP C 901 " pdb=" PB ANP C 901 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.31e+01 ... (remaining 35953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 47258 3.22 - 6.44: 1157 6.44 - 9.67: 169 9.67 - 12.89: 27 12.89 - 16.11: 7 Bond angle restraints: 48618 Sorted by residual: angle pdb=" PB ANP F 901 " pdb=" N3B ANP F 901 " pdb=" PG ANP F 901 " ideal model delta sigma weight residual 126.95 110.84 16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" PB ANP C 901 " pdb=" N3B ANP C 901 " pdb=" PG ANP C 901 " ideal model delta sigma weight residual 126.95 110.85 16.10 3.00e+00 1.11e-01 2.88e+01 angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 110.97 15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" PB ANP E 901 " pdb=" N3B ANP E 901 " pdb=" PG ANP E 901 " ideal model delta sigma weight residual 126.95 110.97 15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" PB ANP A 902 " pdb=" N3B ANP A 902 " pdb=" PG ANP A 902 " ideal model delta sigma weight residual 126.95 111.06 15.89 3.00e+00 1.11e-01 2.80e+01 ... (remaining 48613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 21945 34.81 - 69.62: 298 69.62 - 104.44: 43 104.44 - 139.25: 0 139.25 - 174.06: 4 Dihedral angle restraints: 22290 sinusoidal: 9432 harmonic: 12858 Sorted by residual: dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 114.06 -174.06 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PB ADP D 902 " pdb=" PA ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 113.97 -173.97 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 113.56 -173.56 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 22287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4579 0.099 - 0.197: 765 0.197 - 0.296: 78 0.296 - 0.394: 11 0.394 - 0.493: 3 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CB VAL E 57 " pdb=" CA VAL E 57 " pdb=" CG1 VAL E 57 " pdb=" CG2 VAL E 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CB VAL B 57 " pdb=" CA VAL B 57 " pdb=" CG1 VAL B 57 " pdb=" CG2 VAL B 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CB THR B 549 " pdb=" CA THR B 549 " pdb=" OG1 THR B 549 " pdb=" CG2 THR B 549 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 5433 not shown) Planarity restraints: 6408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 293 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ALA B 293 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA B 293 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU B 294 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 292 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.33e+00 pdb=" C GLU A 292 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU A 292 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 293 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 293 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.29e+00 pdb=" C ALA A 293 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA A 293 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 294 " 0.018 2.00e-02 2.50e+03 ... (remaining 6405 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1552 2.72 - 3.26: 32946 3.26 - 3.81: 51257 3.81 - 4.35: 64483 4.35 - 4.90: 112297 Nonbonded interactions: 262535 Sorted by model distance: nonbonded pdb=" O ALA B 455 " pdb=" ND2 ASN B 460 " model vdw 2.169 3.120 nonbonded pdb=" O ALA E 455 " pdb=" ND2 ASN E 460 " model vdw 2.172 3.120 nonbonded pdb=" OD2 ASP B 373 " pdb=" OG1 THR B 375 " model vdw 2.299 3.040 nonbonded pdb=" OD2 ASP F 373 " pdb=" OG1 THR F 375 " model vdw 2.300 3.040 nonbonded pdb=" OD2 ASP A 373 " pdb=" OG1 THR A 375 " model vdw 2.300 3.040 ... (remaining 262530 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 591 or resid 593 through 766)) selection = (chain 'B' and (resid 18 through 591 or resid 593 through 766)) selection = (chain 'C' and (resid 18 through 591 or resid 593 through 766)) selection = (chain 'D' and (resid 18 through 591 or resid 593 through 766)) selection = (chain 'E' and (resid 18 through 591 or resid 593 through 766)) selection = (chain 'F' and (resid 18 through 591 or resid 593 through 766)) } 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: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 42.210 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.009 0.148 35964 Z= 0.391 Angle : 1.254 16.109 48618 Z= 0.666 Chirality : 0.074 0.493 5436 Planarity : 0.007 0.054 6408 Dihedral : 13.687 174.059 13950 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -3.01 (0.11), residues: 4446 helix: -1.45 (0.11), residues: 1812 sheet: -1.46 (0.18), residues: 624 loop : -2.67 (0.12), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 766 TYR 0.017 0.003 TYR E 143 PHE 0.026 0.003 PHE E 290 TRP 0.013 0.002 TRP D 551 HIS 0.007 0.002 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.39 (35958) covalent geometry : angle 1.25393 / 0.67 (48618) hydrogen bonds : bond 0.19338 / 12.87 ( 1385) hydrogen bonds : angle 6.09266 / 4.19 ( 3951) Misc. bond : bond 0.00207 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 748 time to evaluate : 1.414 Fit side-chains REVERT: A 29 ASP cc_start: 0.8345 (p0) cc_final: 0.8119 (p0) REVERT: A 288 LYS cc_start: 0.8556 (mttp) cc_final: 0.8195 (mtpp) REVERT: A 449 MET cc_start: 0.7938 (tpp) cc_final: 0.7610 (tpp) REVERT: A 460 ASN cc_start: 0.8564 (p0) cc_final: 0.7516 (p0) REVERT: B 113 ARG cc_start: 0.7260 (ttt90) cc_final: 0.7039 (mtm180) REVERT: B 354 ASP cc_start: 0.8569 (t0) cc_final: 0.8197 (t0) REVERT: B 427 MET cc_start: 0.7400 (tpp) cc_final: 0.7150 (mmm) REVERT: B 460 ASN cc_start: 0.8255 (p0) cc_final: 0.7778 (p0) REVERT: B 534 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7147 (tm-30) REVERT: B 701 GLU cc_start: 0.7825 (tp30) cc_final: 0.7408 (tm-30) REVERT: B 744 ARG cc_start: 0.6663 (ttp80) cc_final: 0.6104 (mpt180) REVERT: B 757 MET cc_start: 0.7607 (mmm) cc_final: 0.6917 (mmm) REVERT: C 288 LYS cc_start: 0.8476 (mttp) cc_final: 0.8115 (mtpp) REVERT: C 324 ILE cc_start: 0.9129 (mt) cc_final: 0.8851 (tt) REVERT: C 371 ILE cc_start: 0.9308 (mt) cc_final: 0.9087 (mt) REVERT: C 427 MET cc_start: 0.7625 (tpp) cc_final: 0.7391 (mmm) REVERT: C 460 ASN cc_start: 0.8630 (p0) cc_final: 0.8136 (p0) REVERT: C 464 LEU cc_start: 0.7729 (mm) cc_final: 0.7414 (mm) REVERT: C 491 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7671 (mm-30) REVERT: C 495 TYR cc_start: 0.8626 (m-10) cc_final: 0.8391 (m-10) REVERT: C 744 ARG cc_start: 0.6651 (ttp80) cc_final: 0.6128 (mpt180) REVERT: D 29 ASP cc_start: 0.8331 (p0) cc_final: 0.8111 (p0) REVERT: D 79 ASP cc_start: 0.7248 (p0) cc_final: 0.6776 (p0) REVERT: D 80 GLU cc_start: 0.7249 (pm20) cc_final: 0.7008 (pm20) REVERT: D 288 LYS cc_start: 0.8514 (mttp) cc_final: 0.8136 (mtpp) REVERT: D 449 MET cc_start: 0.7934 (tpp) cc_final: 0.7625 (tpp) REVERT: D 460 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7365 (p0) REVERT: E 113 ARG cc_start: 0.7263 (ttt90) cc_final: 0.7043 (mtm180) REVERT: E 288 LYS cc_start: 0.8468 (mttp) cc_final: 0.8019 (mtpp) REVERT: E 354 ASP cc_start: 0.8584 (t0) cc_final: 0.8213 (t0) REVERT: E 427 MET cc_start: 0.7363 (tpp) cc_final: 0.7145 (mmm) REVERT: E 460 ASN cc_start: 0.8240 (p0) cc_final: 0.7767 (p0) REVERT: E 534 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7100 (tm-30) REVERT: E 701 GLU cc_start: 0.7810 (tp30) cc_final: 0.7387 (tm-30) REVERT: E 744 ARG cc_start: 0.7098 (ttp80) cc_final: 0.6207 (mpt180) REVERT: E 757 MET cc_start: 0.7563 (mmm) cc_final: 0.6811 (mmm) REVERT: F 205 ASP cc_start: 0.7969 (m-30) cc_final: 0.7768 (m-30) REVERT: F 324 ILE cc_start: 0.9124 (mt) cc_final: 0.8848 (tt) REVERT: F 371 ILE cc_start: 0.9323 (mt) cc_final: 0.9115 (mt) REVERT: F 427 MET cc_start: 0.7648 (tpp) cc_final: 0.7424 (mmm) REVERT: F 460 ASN cc_start: 0.8639 (p0) cc_final: 0.7514 (p0) REVERT: F 464 LEU cc_start: 0.7707 (mm) cc_final: 0.7375 (mm) REVERT: F 491 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7630 (mm-30) REVERT: F 495 TYR cc_start: 0.8609 (m-10) cc_final: 0.8366 (m-10) REVERT: F 744 ARG cc_start: 0.6633 (ttp80) cc_final: 0.6120 (mpt180) outliers start: 1 outliers final: 0 residues processed: 748 average time/residue: 0.2425 time to fit residues: 288.9419 Evaluate side-chains 583 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 582 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 460 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.8980 chunk 424 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 HIS B 91 ASN B 443 ASN B 460 ASN C 91 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 HIS D 91 ASN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN E 443 ASN E 460 ASN E 735 HIS F 91 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 735 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119171 restraints weight = 131564.393| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.74 r_work: 0.3294 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35964 Z= 0.114 Angle : 0.612 8.872 48618 Z= 0.299 Chirality : 0.045 0.144 5436 Planarity : 0.005 0.094 6408 Dihedral : 8.225 142.877 4952 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.76 % Allowed : 8.28 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.51 (0.12), residues: 4446 helix: -0.13 (0.12), residues: 1860 sheet: -0.66 (0.19), residues: 606 loop : -1.95 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 635 TYR 0.009 0.001 TYR A 517 PHE 0.009 0.001 PHE A 152 TRP 0.010 0.001 TRP C 454 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (35958) covalent geometry : angle 0.61209 / 0.30 (48618) hydrogen bonds : bond 0.03836 / 2.54 ( 1385) hydrogen bonds : angle 4.20729 / 2.91 ( 3951) Misc. bond : bond 0.00332 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 669 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8649 (p0) cc_final: 0.8380 (p0) REVERT: A 113 ARG cc_start: 0.7428 (mtm180) cc_final: 0.6971 (ttt90) REVERT: A 449 MET cc_start: 0.8398 (tpp) cc_final: 0.7960 (tpp) REVERT: A 460 ASN cc_start: 0.8454 (p0) cc_final: 0.7756 (p0) REVERT: A 484 ASP cc_start: 0.8197 (p0) cc_final: 0.7861 (p0) REVERT: A 488 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 733 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7710 (ttt90) REVERT: B 46 MET cc_start: 0.8178 (ttp) cc_final: 0.7933 (mtm) REVERT: B 70 ILE cc_start: 0.8625 (pt) cc_final: 0.8292 (mm) REVERT: B 333 ASP cc_start: 0.7975 (m-30) cc_final: 0.7755 (m-30) REVERT: B 354 ASP cc_start: 0.8751 (t0) cc_final: 0.8291 (t0) REVERT: B 427 MET cc_start: 0.7252 (tpp) cc_final: 0.6964 (mmm) REVERT: B 460 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8003 (p0) REVERT: B 701 GLU cc_start: 0.8243 (tp30) cc_final: 0.7883 (tm-30) REVERT: B 733 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7694 (ttt90) REVERT: B 744 ARG cc_start: 0.7053 (ttp80) cc_final: 0.6167 (mmt180) REVERT: C 46 MET cc_start: 0.8329 (tpp) cc_final: 0.8109 (mmm) REVERT: C 113 ARG cc_start: 0.7469 (mtm180) cc_final: 0.6808 (ttm-80) REVERT: C 288 LYS cc_start: 0.8732 (mttp) cc_final: 0.8205 (mtpp) REVERT: C 292 GLU cc_start: 0.7672 (mp0) cc_final: 0.7402 (mp0) REVERT: C 427 MET cc_start: 0.7670 (tpp) cc_final: 0.7398 (mmm) REVERT: C 460 ASN cc_start: 0.8413 (p0) cc_final: 0.7640 (p0) REVERT: C 564 ASP cc_start: 0.7757 (m-30) cc_final: 0.7428 (m-30) REVERT: C 701 GLU cc_start: 0.8401 (tp30) cc_final: 0.7906 (tm-30) REVERT: C 733 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7461 (ttt90) REVERT: C 744 ARG cc_start: 0.7074 (ttp80) cc_final: 0.6291 (mpt180) REVERT: C 756 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6980 (tm-30) REVERT: D 29 ASP cc_start: 0.8641 (p0) cc_final: 0.8386 (p0) REVERT: D 113 ARG cc_start: 0.7396 (mtm180) cc_final: 0.6939 (ttt90) REVERT: D 449 MET cc_start: 0.8464 (tpp) cc_final: 0.8093 (tpp) REVERT: D 460 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8135 (p0) REVERT: D 484 ASP cc_start: 0.8316 (p0) cc_final: 0.7963 (p0) REVERT: D 488 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8150 (mm-30) REVERT: D 733 ARG cc_start: 0.8024 (ttm110) cc_final: 0.7613 (ttt90) REVERT: E 46 MET cc_start: 0.8176 (ttp) cc_final: 0.7934 (mtm) REVERT: E 70 ILE cc_start: 0.8640 (pt) cc_final: 0.8312 (mm) REVERT: E 288 LYS cc_start: 0.8592 (mttp) cc_final: 0.8320 (mtpp) REVERT: E 324 ILE cc_start: 0.9371 (mt) cc_final: 0.9166 (tt) REVERT: E 333 ASP cc_start: 0.7958 (m-30) cc_final: 0.7739 (m-30) REVERT: E 354 ASP cc_start: 0.8714 (t0) cc_final: 0.8492 (t0) REVERT: E 427 MET cc_start: 0.7332 (tpp) cc_final: 0.7028 (mmm) REVERT: E 460 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8015 (p0) REVERT: E 701 GLU cc_start: 0.8252 (tp30) cc_final: 0.7884 (tm-30) REVERT: E 733 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7630 (ttt90) REVERT: E 744 ARG cc_start: 0.7676 (ttp80) cc_final: 0.6384 (mmt180) REVERT: F 113 ARG cc_start: 0.7456 (mtm180) cc_final: 0.6788 (ttm-80) REVERT: F 427 MET cc_start: 0.7652 (tpp) cc_final: 0.7382 (mmm) REVERT: F 460 ASN cc_start: 0.8429 (p0) cc_final: 0.7711 (p0) REVERT: F 484 ASP cc_start: 0.8196 (p0) cc_final: 0.7937 (p0) REVERT: F 564 ASP cc_start: 0.7733 (m-30) cc_final: 0.7398 (m-30) REVERT: F 701 GLU cc_start: 0.8400 (tp30) cc_final: 0.7908 (tm-30) REVERT: F 733 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7435 (ttt90) REVERT: F 744 ARG cc_start: 0.6858 (ttp80) cc_final: 0.6304 (mpt180) outliers start: 29 outliers final: 20 residues processed: 692 average time/residue: 0.2354 time to fit residues: 260.0487 Evaluate side-chains 599 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 576 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 568 GLN Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 568 GLN Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 175 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 308 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 417 optimal weight: 0.9990 chunk 300 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 91 ASN B 91 ASN B 460 ASN B 602 ASN B 735 HIS C 91 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN D 91 ASN D 735 HIS E 91 ASN E 460 ASN E 602 ASN F 91 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116397 restraints weight = 127013.294| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.74 r_work: 0.3246 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35964 Z= 0.132 Angle : 0.613 9.192 48618 Z= 0.298 Chirality : 0.045 0.136 5436 Planarity : 0.005 0.101 6408 Dihedral : 8.242 147.687 4952 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.18 % Allowed : 10.41 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 4446 helix: 0.29 (0.12), residues: 1896 sheet: -0.28 (0.20), residues: 600 loop : -1.68 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 635 TYR 0.010 0.001 TYR A 517 PHE 0.010 0.001 PHE A 152 TRP 0.015 0.002 TRP D 454 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (35958) covalent geometry : angle 0.61333 / 0.30 (48618) hydrogen bonds : bond 0.03944 / 2.62 ( 1385) hydrogen bonds : angle 4.00138 / 2.76 ( 3951) Misc. bond : bond 0.00373 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 605 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.8511 (p0) cc_final: 0.7928 (p0) REVERT: A 733 ARG cc_start: 0.8070 (ttm110) cc_final: 0.7657 (ttt90) REVERT: A 757 MET cc_start: 0.7499 (mmm) cc_final: 0.7284 (mmm) REVERT: B 70 ILE cc_start: 0.8629 (pt) cc_final: 0.8356 (mm) REVERT: B 354 ASP cc_start: 0.8715 (t0) cc_final: 0.8507 (t0) REVERT: B 427 MET cc_start: 0.7248 (tpp) cc_final: 0.6755 (mmm) REVERT: B 460 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7953 (p0) REVERT: B 701 GLU cc_start: 0.8203 (tp30) cc_final: 0.7907 (tm-30) REVERT: B 733 ARG cc_start: 0.8293 (ttm110) cc_final: 0.7746 (ttt90) REVERT: B 744 ARG cc_start: 0.7602 (ttp80) cc_final: 0.6668 (mpt180) REVERT: C 113 ARG cc_start: 0.7518 (mtm180) cc_final: 0.6836 (ttt180) REVERT: C 288 LYS cc_start: 0.8750 (mttp) cc_final: 0.8134 (mtpp) REVERT: C 292 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: C 319 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7492 (pp20) REVERT: C 427 MET cc_start: 0.7621 (tpp) cc_final: 0.6911 (mmm) REVERT: C 460 ASN cc_start: 0.8415 (p0) cc_final: 0.7680 (p0) REVERT: C 484 ASP cc_start: 0.8193 (p0) cc_final: 0.7837 (p0) REVERT: C 564 ASP cc_start: 0.7881 (m-30) cc_final: 0.7601 (m-30) REVERT: C 701 GLU cc_start: 0.8399 (tp30) cc_final: 0.7897 (tm-30) REVERT: C 733 ARG cc_start: 0.8004 (ttm110) cc_final: 0.7455 (ttt90) REVERT: C 744 ARG cc_start: 0.7005 (ttp80) cc_final: 0.6332 (mpt180) REVERT: D 29 ASP cc_start: 0.8710 (p0) cc_final: 0.8499 (p0) REVERT: D 460 ASN cc_start: 0.8410 (p0) cc_final: 0.8072 (p0) REVERT: D 733 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7614 (ttt90) REVERT: E 70 ILE cc_start: 0.8650 (pt) cc_final: 0.8379 (mm) REVERT: E 288 LYS cc_start: 0.8579 (mttp) cc_final: 0.8353 (mtpp) REVERT: E 427 MET cc_start: 0.7300 (tpp) cc_final: 0.6800 (mmm) REVERT: E 460 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8186 (p0) REVERT: E 701 GLU cc_start: 0.8201 (tp30) cc_final: 0.7937 (tm-30) REVERT: E 744 ARG cc_start: 0.7861 (ttp80) cc_final: 0.6727 (mmt180) REVERT: F 113 ARG cc_start: 0.7493 (mtm180) cc_final: 0.6813 (ttt180) REVERT: F 319 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7483 (pp20) REVERT: F 427 MET cc_start: 0.7569 (tpp) cc_final: 0.6865 (mmm) REVERT: F 460 ASN cc_start: 0.8428 (p0) cc_final: 0.7738 (p0) REVERT: F 484 ASP cc_start: 0.8296 (p0) cc_final: 0.8070 (p0) REVERT: F 564 ASP cc_start: 0.7848 (m-30) cc_final: 0.7568 (m-30) REVERT: F 701 GLU cc_start: 0.8423 (tp30) cc_final: 0.7908 (tm-30) REVERT: F 733 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7458 (ttt90) REVERT: F 744 ARG cc_start: 0.7015 (ttp80) cc_final: 0.6407 (mpt180) outliers start: 45 outliers final: 29 residues processed: 638 average time/residue: 0.2235 time to fit residues: 232.8639 Evaluate side-chains 609 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 575 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 602 ASN Chi-restraints excluded: chain F residue 756 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 332 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 401 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 331 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 240 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN B 24 ASN B 91 ASN B 460 ASN B 602 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 24 ASN E 91 ASN E 460 ASN E 602 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.142574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115095 restraints weight = 129817.535| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.79 r_work: 0.3230 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 35964 Z= 0.157 Angle : 0.626 11.549 48618 Z= 0.304 Chirality : 0.046 0.138 5436 Planarity : 0.006 0.109 6408 Dihedral : 8.645 168.621 4950 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.08 % Allowed : 11.78 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.78 (0.13), residues: 4446 helix: 0.39 (0.12), residues: 1908 sheet: -0.14 (0.21), residues: 594 loop : -1.55 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 635 TYR 0.011 0.002 TYR C 495 PHE 0.011 0.001 PHE D 152 TRP 0.012 0.002 TRP E 454 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (35958) covalent geometry : angle 0.62643 / 0.30 (48618) hydrogen bonds : bond 0.04132 / 2.75 ( 1385) hydrogen bonds : angle 3.92802 / 2.71 ( 3951) Misc. bond : bond 0.00427 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 587 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.7364 (mtm180) cc_final: 0.6950 (ttt90) REVERT: A 427 MET cc_start: 0.7400 (mmm) cc_final: 0.7186 (mmm) REVERT: A 449 MET cc_start: 0.8296 (tpt) cc_final: 0.8043 (tpp) REVERT: A 460 ASN cc_start: 0.8534 (p0) cc_final: 0.7983 (p0) REVERT: A 733 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7644 (ttt90) REVERT: A 744 ARG cc_start: 0.7301 (ttp80) cc_final: 0.6543 (mpt180) REVERT: B 70 ILE cc_start: 0.8603 (pt) cc_final: 0.8373 (mm) REVERT: B 354 ASP cc_start: 0.8684 (t0) cc_final: 0.8468 (t0) REVERT: B 427 MET cc_start: 0.7391 (tpp) cc_final: 0.6863 (mmm) REVERT: B 460 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8033 (p0) REVERT: B 701 GLU cc_start: 0.8197 (tp30) cc_final: 0.7942 (tm-30) REVERT: B 740 MET cc_start: 0.8392 (tpt) cc_final: 0.8141 (tpt) REVERT: B 744 ARG cc_start: 0.7634 (ttp80) cc_final: 0.6733 (mpt180) REVERT: C 113 ARG cc_start: 0.7517 (mtm180) cc_final: 0.6961 (mtm180) REVERT: C 288 LYS cc_start: 0.8730 (mttp) cc_final: 0.8340 (mtpp) REVERT: C 292 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: C 460 ASN cc_start: 0.8374 (p0) cc_final: 0.7693 (p0) REVERT: C 484 ASP cc_start: 0.8264 (p0) cc_final: 0.7820 (p0) REVERT: C 564 ASP cc_start: 0.7880 (m-30) cc_final: 0.7616 (m-30) REVERT: C 733 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7644 (ttt90) REVERT: C 744 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6351 (mpt180) REVERT: D 113 ARG cc_start: 0.7363 (mtm180) cc_final: 0.6931 (ttt90) REVERT: D 427 MET cc_start: 0.7344 (mmm) cc_final: 0.7133 (mmm) REVERT: D 449 MET cc_start: 0.8298 (tpt) cc_final: 0.8063 (tpp) REVERT: D 460 ASN cc_start: 0.8403 (p0) cc_final: 0.8017 (p0) REVERT: D 733 ARG cc_start: 0.8069 (ttm110) cc_final: 0.7610 (ttt90) REVERT: D 744 ARG cc_start: 0.7310 (ttp80) cc_final: 0.6513 (mpt180) REVERT: D 756 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7327 (tm-30) REVERT: E 70 ILE cc_start: 0.8620 (pt) cc_final: 0.8399 (mm) REVERT: E 288 LYS cc_start: 0.8539 (mttp) cc_final: 0.8258 (mtpp) REVERT: E 427 MET cc_start: 0.7305 (tpp) cc_final: 0.6797 (mmm) REVERT: E 460 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7902 (p0) REVERT: E 701 GLU cc_start: 0.8217 (tp30) cc_final: 0.7946 (tm-30) REVERT: E 740 MET cc_start: 0.8374 (tpt) cc_final: 0.8105 (tpt) REVERT: E 744 ARG cc_start: 0.7853 (ttp80) cc_final: 0.6738 (mmt-90) REVERT: F 113 ARG cc_start: 0.7512 (mtm180) cc_final: 0.6950 (mtm180) REVERT: F 460 ASN cc_start: 0.8379 (p0) cc_final: 0.7698 (p0) REVERT: F 564 ASP cc_start: 0.7869 (m-30) cc_final: 0.7602 (m-30) REVERT: F 701 GLU cc_start: 0.8460 (tp30) cc_final: 0.7974 (tm-30) REVERT: F 733 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7639 (ttt90) REVERT: F 744 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6578 (mpt180) outliers start: 41 outliers final: 32 residues processed: 619 average time/residue: 0.2252 time to fit residues: 228.4239 Evaluate side-chains 585 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 550 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 602 ASN Chi-restraints excluded: chain F residue 756 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 385 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 323 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 256 optimal weight: 0.0270 chunk 48 optimal weight: 0.7980 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN B 91 ASN B 460 ASN B 602 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 91 ASN E 460 ASN E 602 ASN F 91 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117167 restraints weight = 127475.135| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.71 r_work: 0.3260 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35964 Z= 0.112 Angle : 0.585 10.626 48618 Z= 0.282 Chirality : 0.045 0.159 5436 Planarity : 0.004 0.083 6408 Dihedral : 8.418 162.510 4950 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.08 % Allowed : 12.57 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.51 (0.13), residues: 4446 helix: 0.61 (0.12), residues: 1908 sheet: -0.17 (0.20), residues: 642 loop : -1.36 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 635 TYR 0.010 0.001 TYR E 517 PHE 0.009 0.001 PHE F 152 TRP 0.016 0.001 TRP A 454 HIS 0.002 0.000 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (35958) covalent geometry : angle 0.58499 / 0.28 (48618) hydrogen bonds : bond 0.03377 / 2.26 ( 1385) hydrogen bonds : angle 3.73254 / 2.58 ( 3951) Misc. bond : bond 0.00101 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 590 time to evaluate : 1.617 Fit side-chains REVERT: A 294 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8068 (tp30) REVERT: A 449 MET cc_start: 0.8277 (tpt) cc_final: 0.8030 (tpp) REVERT: A 460 ASN cc_start: 0.8233 (p0) cc_final: 0.7673 (p0) REVERT: A 701 GLU cc_start: 0.8289 (tp30) cc_final: 0.8039 (tm-30) REVERT: A 733 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7650 (ttt90) REVERT: A 744 ARG cc_start: 0.7242 (ttp80) cc_final: 0.6563 (mpt180) REVERT: B 294 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8083 (tp30) REVERT: B 354 ASP cc_start: 0.8689 (t0) cc_final: 0.8459 (t0) REVERT: B 427 MET cc_start: 0.7228 (tpp) cc_final: 0.6932 (mmm) REVERT: B 460 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8074 (p0) REVERT: B 701 GLU cc_start: 0.8212 (tp30) cc_final: 0.7969 (tm-30) REVERT: B 740 MET cc_start: 0.8390 (tpt) cc_final: 0.8154 (tpt) REVERT: B 744 ARG cc_start: 0.7588 (ttp80) cc_final: 0.6814 (mpt180) REVERT: C 70 ILE cc_start: 0.8688 (pt) cc_final: 0.8377 (mm) REVERT: C 113 ARG cc_start: 0.7451 (mtm180) cc_final: 0.6880 (mtm180) REVERT: C 288 LYS cc_start: 0.8757 (mttp) cc_final: 0.8360 (mtpp) REVERT: C 292 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: C 319 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7348 (pp20) REVERT: C 427 MET cc_start: 0.7484 (mmm) cc_final: 0.7056 (mmm) REVERT: C 484 ASP cc_start: 0.8245 (p0) cc_final: 0.7762 (p0) REVERT: C 564 ASP cc_start: 0.7888 (m-30) cc_final: 0.7616 (m-30) REVERT: C 733 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7576 (ttt90) REVERT: C 744 ARG cc_start: 0.7018 (ttp80) cc_final: 0.6452 (mpt180) REVERT: D 294 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8063 (tp30) REVERT: D 460 ASN cc_start: 0.8389 (p0) cc_final: 0.8010 (p0) REVERT: D 733 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7618 (ttt90) REVERT: D 744 ARG cc_start: 0.7291 (ttp80) cc_final: 0.6578 (mpt180) REVERT: D 756 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7255 (tm-30) REVERT: E 288 LYS cc_start: 0.8524 (mttp) cc_final: 0.8267 (mtpp) REVERT: E 427 MET cc_start: 0.7160 (tpp) cc_final: 0.6673 (mmm) REVERT: E 460 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7970 (p0) REVERT: E 701 GLU cc_start: 0.8219 (tp30) cc_final: 0.7967 (tm-30) REVERT: E 740 MET cc_start: 0.8416 (tpt) cc_final: 0.8159 (tpt) REVERT: E 744 ARG cc_start: 0.7710 (ttp80) cc_final: 0.6725 (mmt-90) REVERT: F 70 ILE cc_start: 0.8701 (pt) cc_final: 0.8378 (mm) REVERT: F 113 ARG cc_start: 0.7446 (mtm180) cc_final: 0.6878 (mtm180) REVERT: F 319 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7361 (pp20) REVERT: F 427 MET cc_start: 0.7469 (mmm) cc_final: 0.7047 (mmm) REVERT: F 460 ASN cc_start: 0.8323 (p0) cc_final: 0.7921 (p0) REVERT: F 484 ASP cc_start: 0.8140 (p0) cc_final: 0.7788 (p0) REVERT: F 564 ASP cc_start: 0.7907 (m-30) cc_final: 0.7629 (m-30) REVERT: F 733 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7576 (ttt90) REVERT: F 744 ARG cc_start: 0.7021 (ttp80) cc_final: 0.6495 (mpt180) outliers start: 41 outliers final: 26 residues processed: 624 average time/residue: 0.2229 time to fit residues: 229.1755 Evaluate side-chains 590 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 559 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 468 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 388 optimal weight: 5.9990 chunk 429 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 386 optimal weight: 7.9990 chunk 226 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 438 optimal weight: 7.9990 chunk 322 optimal weight: 7.9990 chunk 412 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN B 91 ASN B 460 ASN B 602 ASN C 24 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN D 91 ASN E 91 ASN E 460 ASN E 602 ASN F 91 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116750 restraints weight = 126146.364| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.67 r_work: 0.3260 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35964 Z= 0.123 Angle : 0.588 11.596 48618 Z= 0.283 Chirality : 0.045 0.136 5436 Planarity : 0.005 0.081 6408 Dihedral : 8.226 172.072 4950 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.74 % Allowed : 12.78 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.32 (0.13), residues: 4446 helix: 0.77 (0.13), residues: 1872 sheet: -0.17 (0.20), residues: 678 loop : -1.19 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 635 TYR 0.015 0.001 TYR F 495 PHE 0.009 0.001 PHE D 152 TRP 0.012 0.001 TRP A 454 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (35958) covalent geometry : angle 0.58760 / 0.28 (48618) hydrogen bonds : bond 0.03493 / 2.33 ( 1385) hydrogen bonds : angle 3.70836 / 2.56 ( 3951) Misc. bond : bond 0.00247 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 570 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.7223 (mtm180) cc_final: 0.6773 (ttm-80) REVERT: A 294 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8092 (tp30) REVERT: A 449 MET cc_start: 0.8280 (tpt) cc_final: 0.8037 (tpp) REVERT: A 460 ASN cc_start: 0.8247 (p0) cc_final: 0.7718 (p0) REVERT: A 701 GLU cc_start: 0.8307 (tp30) cc_final: 0.8055 (tm-30) REVERT: A 733 ARG cc_start: 0.8213 (ttm110) cc_final: 0.7614 (ttt90) REVERT: A 744 ARG cc_start: 0.7413 (ttp80) cc_final: 0.6612 (mpt180) REVERT: B 427 MET cc_start: 0.7227 (tpp) cc_final: 0.6948 (mmm) REVERT: B 460 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7993 (p0) REVERT: B 701 GLU cc_start: 0.8210 (tp30) cc_final: 0.7963 (tm-30) REVERT: B 740 MET cc_start: 0.8359 (tpt) cc_final: 0.8138 (tpt) REVERT: B 744 ARG cc_start: 0.7557 (ttp80) cc_final: 0.6771 (mpt180) REVERT: C 70 ILE cc_start: 0.8718 (pt) cc_final: 0.8386 (mm) REVERT: C 113 ARG cc_start: 0.7443 (mtm180) cc_final: 0.6881 (mtm180) REVERT: C 288 LYS cc_start: 0.8767 (mttp) cc_final: 0.8356 (mtpp) REVERT: C 292 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: C 319 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7337 (pp20) REVERT: C 427 MET cc_start: 0.7482 (mmm) cc_final: 0.7052 (mmm) REVERT: C 484 ASP cc_start: 0.8268 (p0) cc_final: 0.8054 (p0) REVERT: C 564 ASP cc_start: 0.7851 (m-30) cc_final: 0.7591 (m-30) REVERT: C 733 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7077 (ttt90) REVERT: C 744 ARG cc_start: 0.7054 (ttp80) cc_final: 0.6569 (mpt180) REVERT: D 113 ARG cc_start: 0.7208 (mtm180) cc_final: 0.6777 (ttt-90) REVERT: D 449 MET cc_start: 0.8297 (tpt) cc_final: 0.8075 (tpp) REVERT: D 460 ASN cc_start: 0.8417 (p0) cc_final: 0.8048 (p0) REVERT: D 701 GLU cc_start: 0.8225 (tp30) cc_final: 0.8001 (tm-30) REVERT: D 733 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7660 (ttt90) REVERT: D 744 ARG cc_start: 0.7311 (ttp80) cc_final: 0.6587 (mpt180) REVERT: D 756 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7279 (tm-30) REVERT: E 288 LYS cc_start: 0.8534 (mttp) cc_final: 0.8284 (mtpp) REVERT: E 427 MET cc_start: 0.7141 (tpp) cc_final: 0.6865 (mmm) REVERT: E 460 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7987 (p0) REVERT: E 701 GLU cc_start: 0.8222 (tp30) cc_final: 0.7967 (tm-30) REVERT: E 740 MET cc_start: 0.8343 (tpt) cc_final: 0.8119 (tpt) REVERT: E 744 ARG cc_start: 0.7690 (ttp80) cc_final: 0.6762 (mmt-90) REVERT: F 70 ILE cc_start: 0.8711 (pt) cc_final: 0.8388 (mm) REVERT: F 113 ARG cc_start: 0.7440 (mtm180) cc_final: 0.6871 (mtm180) REVERT: F 319 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7330 (pp20) REVERT: F 427 MET cc_start: 0.7476 (mmm) cc_final: 0.7032 (mmm) REVERT: F 460 ASN cc_start: 0.8280 (p0) cc_final: 0.7873 (p0) REVERT: F 484 ASP cc_start: 0.8212 (p0) cc_final: 0.7835 (p0) REVERT: F 564 ASP cc_start: 0.7887 (m-30) cc_final: 0.7609 (m-30) REVERT: F 733 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7060 (ttt90) REVERT: F 744 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6454 (mpt180) outliers start: 66 outliers final: 46 residues processed: 620 average time/residue: 0.2213 time to fit residues: 225.9769 Evaluate side-chains 605 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 554 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 602 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 237 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 310 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 379 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN B 24 ASN B 91 ASN B 460 ASN C 24 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN D 91 ASN E 24 ASN E 91 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN F 91 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.139529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112185 restraints weight = 126203.708| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.74 r_work: 0.3190 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 35964 Z= 0.237 Angle : 0.707 15.594 48618 Z= 0.342 Chirality : 0.049 0.152 5436 Planarity : 0.005 0.065 6408 Dihedral : 8.580 177.776 4950 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.05 % Allowed : 13.41 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.69 (0.13), residues: 4446 helix: 0.28 (0.12), residues: 1908 sheet: -0.13 (0.21), residues: 594 loop : -1.26 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 635 TYR 0.022 0.002 TYR F 495 PHE 0.016 0.002 PHE F 682 TRP 0.012 0.002 TRP F 454 HIS 0.005 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (35958) covalent geometry : angle 0.70690 / 0.34 (48618) hydrogen bonds : bond 0.05060 / 3.39 ( 1385) hydrogen bonds : angle 4.18038 / 2.88 ( 3951) Misc. bond : bond 0.00304 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 544 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 449 MET cc_start: 0.8294 (tpt) cc_final: 0.8077 (tpp) REVERT: A 460 ASN cc_start: 0.8397 (p0) cc_final: 0.7956 (p0) REVERT: A 701 GLU cc_start: 0.8381 (tp30) cc_final: 0.8117 (tm-30) REVERT: A 733 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7446 (ttt90) REVERT: A 744 ARG cc_start: 0.7526 (ttp80) cc_final: 0.6733 (mpt180) REVERT: B 460 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8118 (p0) REVERT: B 701 GLU cc_start: 0.8299 (tp30) cc_final: 0.7938 (tm-30) REVERT: C 98 ASP cc_start: 0.8833 (m-30) cc_final: 0.8626 (m-30) REVERT: C 113 ARG cc_start: 0.7606 (mtm180) cc_final: 0.7183 (mtm180) REVERT: C 288 LYS cc_start: 0.8691 (mttp) cc_final: 0.8350 (mtpp) REVERT: C 319 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: C 564 ASP cc_start: 0.7901 (m-30) cc_final: 0.7616 (m-30) REVERT: C 744 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6449 (mpt180) REVERT: D 449 MET cc_start: 0.8369 (tpt) cc_final: 0.8131 (tpp) REVERT: D 460 ASN cc_start: 0.8498 (p0) cc_final: 0.8142 (p0) REVERT: D 701 GLU cc_start: 0.8305 (tp30) cc_final: 0.8001 (tm-30) REVERT: D 744 ARG cc_start: 0.7526 (ttp80) cc_final: 0.6720 (mpt180) REVERT: E 288 LYS cc_start: 0.8496 (mttp) cc_final: 0.8269 (mtpp) REVERT: E 427 MET cc_start: 0.7381 (tpp) cc_final: 0.6849 (mmm) REVERT: E 460 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.8056 (p0) REVERT: E 701 GLU cc_start: 0.8310 (tp30) cc_final: 0.7988 (tm-30) REVERT: E 744 ARG cc_start: 0.7711 (ttp80) cc_final: 0.6583 (mmt-90) REVERT: F 113 ARG cc_start: 0.7605 (mtm180) cc_final: 0.7185 (mtm180) REVERT: F 233 ILE cc_start: 0.9222 (pt) cc_final: 0.8890 (mt) REVERT: F 319 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: F 458 GLN cc_start: 0.8382 (pt0) cc_final: 0.8102 (pt0) REVERT: F 460 ASN cc_start: 0.8477 (p0) cc_final: 0.7820 (p0) REVERT: F 484 ASP cc_start: 0.8253 (p0) cc_final: 0.7878 (p0) REVERT: F 564 ASP cc_start: 0.7893 (m-30) cc_final: 0.7601 (m-30) REVERT: F 744 ARG cc_start: 0.7299 (ttp80) cc_final: 0.6511 (mpt180) outliers start: 78 outliers final: 61 residues processed: 604 average time/residue: 0.2199 time to fit residues: 219.2372 Evaluate side-chains 593 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 528 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain E residue 756 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 602 ASN Chi-restraints excluded: chain F residue 756 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 98 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 390 optimal weight: 0.7980 chunk 354 optimal weight: 3.9990 chunk 338 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN B 91 ASN B 460 ASN B 602 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN D 91 ASN E 91 ASN E 460 ASN E 602 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.137952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111604 restraints weight = 130294.942| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.72 r_work: 0.3188 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35964 Z= 0.147 Angle : 0.633 16.666 48618 Z= 0.302 Chirality : 0.046 0.144 5436 Planarity : 0.005 0.090 6408 Dihedral : 8.333 179.525 4950 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.79 % Allowed : 13.93 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.52 (0.13), residues: 4446 helix: 0.46 (0.12), residues: 1908 sheet: -0.21 (0.20), residues: 642 loop : -1.16 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 635 TYR 0.017 0.001 TYR F 495 PHE 0.013 0.001 PHE F 682 TRP 0.011 0.001 TRP A 454 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (35958) covalent geometry : angle 0.63335 / 0.30 (48618) hydrogen bonds : bond 0.03897 / 2.61 ( 1385) hydrogen bonds : angle 3.89660 / 2.69 ( 3951) Misc. bond : bond 0.00180 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 535 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.7263 (mtm180) cc_final: 0.6745 (ttm-80) REVERT: A 449 MET cc_start: 0.8219 (tpt) cc_final: 0.8009 (tpp) REVERT: A 460 ASN cc_start: 0.8410 (p0) cc_final: 0.8048 (p0) REVERT: A 733 ARG cc_start: 0.8288 (ttm110) cc_final: 0.7698 (ttt90) REVERT: A 744 ARG cc_start: 0.7612 (ttp80) cc_final: 0.6778 (mpt180) REVERT: B 46 MET cc_start: 0.8268 (ttp) cc_final: 0.8027 (mtm) REVERT: B 442 MET cc_start: 0.8372 (tpp) cc_final: 0.8171 (tpp) REVERT: B 460 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8132 (p0) REVERT: B 701 GLU cc_start: 0.8228 (tp30) cc_final: 0.7903 (tm-30) REVERT: B 744 ARG cc_start: 0.7695 (ttp80) cc_final: 0.6767 (mpt180) REVERT: C 98 ASP cc_start: 0.8835 (m-30) cc_final: 0.8613 (m-30) REVERT: C 113 ARG cc_start: 0.7550 (mtm180) cc_final: 0.7157 (mtm180) REVERT: C 319 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7342 (pp20) REVERT: C 564 ASP cc_start: 0.7830 (m-30) cc_final: 0.7548 (m-30) REVERT: C 733 ARG cc_start: 0.7915 (ttm110) cc_final: 0.6904 (ttt180) REVERT: C 744 ARG cc_start: 0.7233 (ttp80) cc_final: 0.6476 (mpt180) REVERT: D 113 ARG cc_start: 0.7269 (mtm180) cc_final: 0.6819 (ttt-90) REVERT: D 449 MET cc_start: 0.8216 (tpt) cc_final: 0.7993 (tpp) REVERT: D 460 ASN cc_start: 0.8465 (p0) cc_final: 0.8119 (p0) REVERT: D 701 GLU cc_start: 0.8245 (tp30) cc_final: 0.8000 (tm-30) REVERT: D 733 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7697 (ttt90) REVERT: D 744 ARG cc_start: 0.7651 (ttp80) cc_final: 0.6773 (mpt180) REVERT: E 46 MET cc_start: 0.8241 (ttp) cc_final: 0.7994 (mtm) REVERT: E 288 LYS cc_start: 0.8544 (mttp) cc_final: 0.8320 (mtpp) REVERT: E 427 MET cc_start: 0.7336 (tpp) cc_final: 0.6792 (mmm) REVERT: E 460 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8094 (p0) REVERT: E 701 GLU cc_start: 0.8223 (tp30) cc_final: 0.7915 (tm-30) REVERT: E 744 ARG cc_start: 0.7701 (ttp80) cc_final: 0.6586 (mmt-90) REVERT: F 113 ARG cc_start: 0.7538 (mtm180) cc_final: 0.7151 (mtm180) REVERT: F 233 ILE cc_start: 0.9181 (pt) cc_final: 0.8823 (mt) REVERT: F 319 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7356 (pp20) REVERT: F 460 ASN cc_start: 0.8378 (p0) cc_final: 0.8070 (p0) REVERT: F 484 ASP cc_start: 0.8249 (p0) cc_final: 0.7876 (p0) REVERT: F 564 ASP cc_start: 0.7822 (m-30) cc_final: 0.7534 (m-30) REVERT: F 744 ARG cc_start: 0.7255 (ttp80) cc_final: 0.6542 (mpt180) outliers start: 68 outliers final: 56 residues processed: 589 average time/residue: 0.2205 time to fit residues: 215.2628 Evaluate side-chains 594 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 534 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 602 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 332 optimal weight: 0.0570 chunk 227 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 331 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 356 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN B 91 ASN B 460 ASN C 91 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN D 91 ASN E 91 ASN E 460 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116250 restraints weight = 116559.635| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.52 r_work: 0.3258 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35964 Z= 0.138 Angle : 0.636 17.743 48618 Z= 0.301 Chirality : 0.046 0.153 5436 Planarity : 0.005 0.092 6408 Dihedral : 8.340 176.864 4950 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.95 % Allowed : 14.01 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.44 (0.13), residues: 4446 helix: 0.51 (0.12), residues: 1908 sheet: -0.16 (0.20), residues: 642 loop : -1.10 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 635 TYR 0.017 0.001 TYR F 495 PHE 0.013 0.001 PHE F 682 TRP 0.010 0.001 TRP C 454 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (35958) covalent geometry : angle 0.63581 / 0.30 (48618) hydrogen bonds : bond 0.03768 / 2.52 ( 1385) hydrogen bonds : angle 3.82850 / 2.65 ( 3951) Misc. bond : bond 0.00214 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 539 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.7270 (mtm180) cc_final: 0.6751 (ttm-80) REVERT: A 449 MET cc_start: 0.8278 (tpt) cc_final: 0.8075 (tpp) REVERT: A 460 ASN cc_start: 0.8377 (p0) cc_final: 0.7980 (p0) REVERT: A 701 GLU cc_start: 0.8370 (tp30) cc_final: 0.8100 (tm-30) REVERT: A 733 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7698 (ttt90) REVERT: A 744 ARG cc_start: 0.7545 (ttp80) cc_final: 0.6789 (mpt180) REVERT: B 46 MET cc_start: 0.8203 (ttp) cc_final: 0.7955 (mtm) REVERT: B 427 MET cc_start: 0.7418 (mmm) cc_final: 0.7082 (mmt) REVERT: B 460 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7942 (p0) REVERT: B 701 GLU cc_start: 0.8210 (tp30) cc_final: 0.7953 (tm-30) REVERT: B 744 ARG cc_start: 0.7709 (ttp80) cc_final: 0.6794 (mpt180) REVERT: C 113 ARG cc_start: 0.7544 (mtm180) cc_final: 0.7170 (mtm180) REVERT: C 305 GLU cc_start: 0.7963 (mp0) cc_final: 0.7729 (mp0) REVERT: C 319 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7333 (pp20) REVERT: C 564 ASP cc_start: 0.7863 (m-30) cc_final: 0.7577 (m-30) REVERT: C 733 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7073 (ttt180) REVERT: C 744 ARG cc_start: 0.7242 (ttp80) cc_final: 0.6569 (mpt180) REVERT: D 113 ARG cc_start: 0.7262 (mtm180) cc_final: 0.6747 (ttm-80) REVERT: D 460 ASN cc_start: 0.8438 (p0) cc_final: 0.8069 (p0) REVERT: D 701 GLU cc_start: 0.8305 (tp30) cc_final: 0.8025 (tm-30) REVERT: D 733 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7699 (ttt90) REVERT: D 744 ARG cc_start: 0.7501 (ttp80) cc_final: 0.6723 (mpt180) REVERT: E 46 MET cc_start: 0.8202 (ttp) cc_final: 0.7963 (mtm) REVERT: E 281 GLU cc_start: 0.7464 (pm20) cc_final: 0.7211 (pm20) REVERT: E 427 MET cc_start: 0.7358 (tpp) cc_final: 0.6844 (mmm) REVERT: E 460 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7871 (p0) REVERT: E 701 GLU cc_start: 0.8184 (tp30) cc_final: 0.7944 (tm-30) REVERT: E 744 ARG cc_start: 0.7717 (ttp80) cc_final: 0.6635 (mmt-90) REVERT: F 113 ARG cc_start: 0.7558 (mtm180) cc_final: 0.7189 (mtm180) REVERT: F 233 ILE cc_start: 0.9134 (pt) cc_final: 0.8808 (mt) REVERT: F 319 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7371 (pp20) REVERT: F 460 ASN cc_start: 0.8327 (p0) cc_final: 0.7994 (p0) REVERT: F 484 ASP cc_start: 0.8199 (p0) cc_final: 0.7795 (p0) REVERT: F 564 ASP cc_start: 0.7894 (m-30) cc_final: 0.7595 (m-30) REVERT: F 744 ARG cc_start: 0.7331 (ttp80) cc_final: 0.6626 (mpt180) outliers start: 74 outliers final: 59 residues processed: 599 average time/residue: 0.2188 time to fit residues: 216.4253 Evaluate side-chains 594 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 531 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 602 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 442 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 437 optimal weight: 0.9980 chunk 412 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 377 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN B 91 ASN B 460 ASN C 91 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN D 91 ASN E 91 ASN E 460 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.147203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121057 restraints weight = 130964.418| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.64 r_work: 0.3333 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35964 Z= 0.115 Angle : 0.625 17.077 48618 Z= 0.295 Chirality : 0.045 0.156 5436 Planarity : 0.005 0.139 6408 Dihedral : 8.324 174.991 4950 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.71 % Allowed : 14.46 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.33 (0.13), residues: 4446 helix: 0.59 (0.12), residues: 1908 sheet: -0.08 (0.20), residues: 642 loop : -1.05 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG F 635 TYR 0.011 0.001 TYR E 517 PHE 0.011 0.001 PHE F 682 TRP 0.010 0.001 TRP C 454 HIS 0.002 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (35958) covalent geometry : angle 0.62541 / 0.30 (48618) hydrogen bonds : bond 0.03430 / 2.29 ( 1385) hydrogen bonds : angle 3.76226 / 2.60 ( 3951) Misc. bond : bond 0.00297 / 0.13 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8892 Ramachandran restraints generated. 4446 Oldfield, 0 Emsley, 4446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 544 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ARG cc_start: 0.7156 (mtm180) cc_final: 0.6652 (ttm-80) REVERT: A 460 ASN cc_start: 0.8228 (p0) cc_final: 0.7850 (p0) REVERT: A 701 GLU cc_start: 0.8317 (tp30) cc_final: 0.8112 (tm-30) REVERT: A 733 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7692 (ttt90) REVERT: A 744 ARG cc_start: 0.7575 (ttp80) cc_final: 0.6892 (mpt180) REVERT: B 427 MET cc_start: 0.7293 (mmm) cc_final: 0.6950 (mmt) REVERT: B 701 GLU cc_start: 0.8145 (tp30) cc_final: 0.7785 (tm-30) REVERT: B 733 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7915 (ttt90) REVERT: B 744 ARG cc_start: 0.7409 (ttp80) cc_final: 0.6741 (mpt180) REVERT: C 70 ILE cc_start: 0.8726 (pt) cc_final: 0.8399 (mm) REVERT: C 113 ARG cc_start: 0.7460 (mtm180) cc_final: 0.7115 (mtm180) REVERT: C 305 GLU cc_start: 0.7929 (mp0) cc_final: 0.7698 (mp0) REVERT: C 319 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7417 (pp20) REVERT: C 427 MET cc_start: 0.7450 (mmm) cc_final: 0.7181 (mmm) REVERT: C 564 ASP cc_start: 0.7793 (m-30) cc_final: 0.7516 (m-30) REVERT: C 733 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7446 (ttt90) REVERT: C 744 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6690 (mpt180) REVERT: D 113 ARG cc_start: 0.7141 (mtm180) cc_final: 0.6642 (ttm-80) REVERT: D 305 GLU cc_start: 0.7775 (mp0) cc_final: 0.7562 (mp0) REVERT: D 460 ASN cc_start: 0.8350 (p0) cc_final: 0.7948 (p0) REVERT: D 701 GLU cc_start: 0.8301 (tp30) cc_final: 0.8035 (tm-30) REVERT: D 733 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7705 (ttt90) REVERT: D 744 ARG cc_start: 0.7502 (ttp80) cc_final: 0.6814 (mpt180) REVERT: D 756 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7444 (tm-30) REVERT: E 427 MET cc_start: 0.7222 (tpp) cc_final: 0.6956 (mmm) REVERT: E 744 ARG cc_start: 0.7696 (ttp80) cc_final: 0.6727 (mmt-90) REVERT: F 70 ILE cc_start: 0.8715 (pt) cc_final: 0.8393 (mm) REVERT: F 113 ARG cc_start: 0.7462 (mtm180) cc_final: 0.7117 (mtm180) REVERT: F 233 ILE cc_start: 0.9079 (pt) cc_final: 0.8678 (mt) REVERT: F 305 GLU cc_start: 0.7905 (mp0) cc_final: 0.7651 (mp0) REVERT: F 319 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7418 (pp20) REVERT: F 427 MET cc_start: 0.7458 (mmm) cc_final: 0.7126 (mmm) REVERT: F 460 ASN cc_start: 0.8221 (p0) cc_final: 0.7504 (p0) REVERT: F 484 ASP cc_start: 0.8065 (p0) cc_final: 0.7666 (p0) REVERT: F 564 ASP cc_start: 0.7785 (m-30) cc_final: 0.7498 (m-30) REVERT: F 744 ARG cc_start: 0.7288 (ttp80) cc_final: 0.6729 (mpt180) outliers start: 65 outliers final: 52 residues processed: 596 average time/residue: 0.2137 time to fit residues: 211.1864 Evaluate side-chains 588 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 534 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 683 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 602 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 214 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 138 optimal weight: 0.0970 chunk 209 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 229 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 334 optimal weight: 0.4980 chunk 317 optimal weight: 0.2980 chunk 401 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN B 91 ASN B 602 ASN C 91 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 568 GLN D 91 ASN E 91 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 91 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121875 restraints weight = 118042.550| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.42 r_work: 0.3367 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35964 Z= 0.108 Angle : 0.622 17.803 48618 Z= 0.293 Chirality : 0.045 0.149 5436 Planarity : 0.005 0.119 6408 Dihedral : 8.250 174.774 4950 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.55 % Allowed : 14.70 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.22 (0.13), residues: 4446 helix: 0.70 (0.12), residues: 1908 sheet: 0.01 (0.21), residues: 642 loop : -1.02 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG C 635 TYR 0.011 0.001 TYR E 495 PHE 0.010 0.001 PHE F 682 TRP 0.008 0.001 TRP C 454 HIS 0.002 0.000 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (35958) covalent geometry : angle 0.62152 / 0.29 (48618) hydrogen bonds : bond 0.03196 / 2.14 ( 1385) hydrogen bonds : angle 3.68589 / 2.55 ( 3951) Misc. bond : bond 0.00362 / 0.17 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9090.74 seconds wall clock time: 156 minutes 10.85 seconds (9370.85 seconds total)