Starting phenix.real_space_refine on Tue Aug 26 20:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cka_16694/08_2025/8cka_16694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cka_16694/08_2025/8cka_16694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cka_16694/08_2025/8cka_16694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cka_16694/08_2025/8cka_16694.map" model { file = "/net/cci-nas-00/data/ceres_data/8cka_16694/08_2025/8cka_16694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cka_16694/08_2025/8cka_16694.cif" } resolution = 2.52 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= 0.003 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 25164 2.51 5 N 7158 2.21 5 O 8400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40770 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3686 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 474} Chain: "B" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3109 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: C, E, G, I, K, D, F, H, J, L Time building chain proxies: 6.30, per 1000 atoms: 0.15 Number of scatterers: 40770 At special positions: 0 Unit cell: (252.252, 271.908, 126.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 8400 8.00 N 7158 7.00 C 25164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 554 " - pdb=" SG CYS B 666 " distance=2.08 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 168 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 168 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 168 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 168 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 554 " - pdb=" SG CYS D 666 " distance=2.08 Simple disulfide: pdb=" SG CYS F 554 " - pdb=" SG CYS F 666 " distance=2.07 Simple disulfide: pdb=" SG CYS H 554 " - pdb=" SG CYS H 666 " distance=2.08 Simple disulfide: pdb=" SG CYS J 554 " - pdb=" SG CYS J 666 " distance=2.08 Simple disulfide: pdb=" SG CYS L 554 " - pdb=" SG CYS L 666 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9852 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 102 sheets defined 7.6% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN A 443 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 598 through 600 No H-bonds generated for 'chain 'A' and resid 598 through 600' Processing helix chain 'B' and resid 598 through 600 No H-bonds generated for 'chain 'B' and resid 598 through 600' Processing helix chain 'B' and resid 797 through 800 Processing helix chain 'B' and resid 841 through 854 Processing helix chain 'B' and resid 856 through 861 Processing helix chain 'B' and resid 865 through 875 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN C 443 " --> pdb=" O ALA C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 461 Processing helix chain 'C' and resid 598 through 600 No H-bonds generated for 'chain 'C' and resid 598 through 600' Processing helix chain 'D' and resid 598 through 600 No H-bonds generated for 'chain 'D' and resid 598 through 600' Processing helix chain 'D' and resid 797 through 800 Processing helix chain 'D' and resid 841 through 854 Processing helix chain 'D' and resid 856 through 861 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN E 443 " --> pdb=" O ALA E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 461 Processing helix chain 'E' and resid 598 through 600 No H-bonds generated for 'chain 'E' and resid 598 through 600' Processing helix chain 'F' and resid 598 through 600 No H-bonds generated for 'chain 'F' and resid 598 through 600' Processing helix chain 'F' and resid 797 through 800 Processing helix chain 'F' and resid 841 through 854 Processing helix chain 'F' and resid 856 through 861 Processing helix chain 'F' and resid 865 through 875 Processing helix chain 'G' and resid 234 through 237 Processing helix chain 'G' and resid 309 through 311 No H-bonds generated for 'chain 'G' and resid 309 through 311' Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN G 443 " --> pdb=" O ALA G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 598 through 600 No H-bonds generated for 'chain 'G' and resid 598 through 600' Processing helix chain 'H' and resid 598 through 600 No H-bonds generated for 'chain 'H' and resid 598 through 600' Processing helix chain 'H' and resid 797 through 800 Processing helix chain 'H' and resid 841 through 854 Processing helix chain 'H' and resid 856 through 861 Processing helix chain 'H' and resid 865 through 875 Processing helix chain 'I' and resid 234 through 237 Processing helix chain 'I' and resid 309 through 311 No H-bonds generated for 'chain 'I' and resid 309 through 311' Processing helix chain 'I' and resid 333 through 337 Processing helix chain 'I' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN I 443 " --> pdb=" O ALA I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 461 Processing helix chain 'I' and resid 598 through 600 No H-bonds generated for 'chain 'I' and resid 598 through 600' Processing helix chain 'J' and resid 598 through 600 No H-bonds generated for 'chain 'J' and resid 598 through 600' Processing helix chain 'J' and resid 797 through 800 Processing helix chain 'J' and resid 841 through 854 Processing helix chain 'J' and resid 856 through 861 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'K' and resid 234 through 237 Processing helix chain 'K' and resid 309 through 311 No H-bonds generated for 'chain 'K' and resid 309 through 311' Processing helix chain 'K' and resid 333 through 337 Processing helix chain 'K' and resid 439 through 443 removed outlier: 3.729A pdb=" N ASN K 443 " --> pdb=" O ALA K 440 " (cutoff:3.500A) Processing helix chain 'K' and resid 450 through 461 Processing helix chain 'K' and resid 598 through 600 No H-bonds generated for 'chain 'K' and resid 598 through 600' Processing helix chain 'L' and resid 598 through 600 No H-bonds generated for 'chain 'L' and resid 598 through 600' Processing helix chain 'L' and resid 797 through 800 Processing helix chain 'L' and resid 841 through 854 Processing helix chain 'L' and resid 856 through 861 Processing helix chain 'L' and resid 865 through 875 Processing sheet with id=1, first strand: chain 'A' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE A 138 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 158 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 146 through 148 removed outlier: 6.594A pdb=" N ALA A 147 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=4, first strand: chain 'A' and resid 252 through 260 removed outlier: 25.580A pdb=" N GLY A 268 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR A 354 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL A 270 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE A 272 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 315 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 294 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 313 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 369 through 373 Processing sheet with id=6, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR A 391 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR A 391 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 532 through 533 Processing sheet with id=9, first strand: chain 'A' and resid 537 through 540 Processing sheet with id=10, first strand: chain 'A' and resid 554 through 555 removed outlier: 4.439A pdb=" N PHE A 583 " --> pdb=" O ILE A 590 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 532 through 533 Processing sheet with id=12, first strand: chain 'B' and resid 537 through 540 Processing sheet with id=13, first strand: chain 'B' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE B 583 " --> pdb=" O ILE B 590 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 637 through 640 Processing sheet with id=15, first strand: chain 'B' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE B 649 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR B 728 " --> pdb=" O TRP B 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP B 675 " --> pdb=" O TYR B 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG B 730 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU B 673 " --> pdb=" O ARG B 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 732 " --> pdb=" O THR B 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 671 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 734 " --> pdb=" O TYR B 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 698 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP B 675 " --> pdb=" O GLN B 696 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN B 696 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 764 through 768 Processing sheet with id=17, first strand: chain 'B' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA B 836 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER B 888 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 834 " --> pdb=" O SER B 888 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN B 927 " --> pdb=" O ARG B 839 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE C 138 " --> pdb=" O THR C 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR C 158 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.594A pdb=" N ALA C 147 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 230 through 232 Processing sheet with id=21, first strand: chain 'C' and resid 252 through 260 removed outlier: 25.580A pdb=" N GLY C 268 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL C 270 " --> pdb=" O TYR C 354 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE C 272 " --> pdb=" O PRO C 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 315 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU C 294 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 313 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'C' and resid 369 through 373 Processing sheet with id=23, first strand: chain 'C' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR C 391 " --> pdb=" O ARG C 525 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'C' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR C 391 " --> pdb=" O ARG C 525 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'C' and resid 532 through 533 Processing sheet with id=26, first strand: chain 'C' and resid 537 through 540 Processing sheet with id=27, first strand: chain 'C' and resid 554 through 555 removed outlier: 4.438A pdb=" N PHE C 583 " --> pdb=" O ILE C 590 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'D' and resid 532 through 533 Processing sheet with id=29, first strand: chain 'D' and resid 537 through 540 Processing sheet with id=30, first strand: chain 'D' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE D 583 " --> pdb=" O ILE D 590 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'D' and resid 637 through 640 Processing sheet with id=32, first strand: chain 'D' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE D 649 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR D 728 " --> pdb=" O TRP D 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP D 675 " --> pdb=" O TYR D 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG D 730 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU D 673 " --> pdb=" O ARG D 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU D 732 " --> pdb=" O THR D 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR D 671 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 734 " --> pdb=" O TYR D 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 698 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP D 675 " --> pdb=" O GLN D 696 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN D 696 " --> pdb=" O TRP D 675 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'D' and resid 764 through 768 Processing sheet with id=34, first strand: chain 'D' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA D 836 " --> pdb=" O LEU D 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER D 888 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 834 " --> pdb=" O SER D 888 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN D 927 " --> pdb=" O ARG D 839 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'E' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE E 138 " --> pdb=" O THR E 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR E 158 " --> pdb=" O ILE E 138 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.595A pdb=" N ALA E 147 " --> pdb=" O LYS E 219 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'E' and resid 230 through 232 Processing sheet with id=38, first strand: chain 'E' and resid 252 through 260 removed outlier: 25.579A pdb=" N GLY E 268 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR E 354 " --> pdb=" O GLY E 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL E 270 " --> pdb=" O TYR E 354 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE E 272 " --> pdb=" O PRO E 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG E 315 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU E 294 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL E 313 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'E' and resid 369 through 373 Processing sheet with id=40, first strand: chain 'E' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR E 391 " --> pdb=" O ARG E 525 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'E' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR E 391 " --> pdb=" O ARG E 525 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'E' and resid 532 through 533 Processing sheet with id=43, first strand: chain 'E' and resid 537 through 540 Processing sheet with id=44, first strand: chain 'E' and resid 554 through 555 removed outlier: 4.439A pdb=" N PHE E 583 " --> pdb=" O ILE E 590 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'F' and resid 532 through 533 Processing sheet with id=46, first strand: chain 'F' and resid 537 through 540 Processing sheet with id=47, first strand: chain 'F' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE F 583 " --> pdb=" O ILE F 590 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'F' and resid 637 through 640 Processing sheet with id=49, first strand: chain 'F' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE F 649 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR F 728 " --> pdb=" O TRP F 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP F 675 " --> pdb=" O TYR F 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG F 730 " --> pdb=" O LEU F 673 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU F 673 " --> pdb=" O ARG F 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU F 732 " --> pdb=" O THR F 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR F 671 " --> pdb=" O LEU F 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL F 734 " --> pdb=" O TYR F 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA F 698 " --> pdb=" O LEU F 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP F 675 " --> pdb=" O GLN F 696 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN F 696 " --> pdb=" O TRP F 675 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'F' and resid 764 through 768 Processing sheet with id=51, first strand: chain 'F' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA F 836 " --> pdb=" O LEU F 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER F 888 " --> pdb=" O VAL F 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL F 834 " --> pdb=" O SER F 888 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN F 927 " --> pdb=" O ARG F 839 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'G' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE G 138 " --> pdb=" O THR G 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR G 158 " --> pdb=" O ILE G 138 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'G' and resid 146 through 148 removed outlier: 6.594A pdb=" N ALA G 147 " --> pdb=" O LYS G 219 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'G' and resid 230 through 232 Processing sheet with id=55, first strand: chain 'G' and resid 252 through 260 removed outlier: 25.580A pdb=" N GLY G 268 " --> pdb=" O VAL G 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR G 354 " --> pdb=" O GLY G 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL G 270 " --> pdb=" O TYR G 354 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE G 272 " --> pdb=" O PRO G 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG G 315 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU G 294 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL G 313 " --> pdb=" O LEU G 294 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'G' and resid 369 through 373 Processing sheet with id=57, first strand: chain 'G' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR G 391 " --> pdb=" O ARG G 525 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'G' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR G 391 " --> pdb=" O ARG G 525 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'G' and resid 532 through 533 Processing sheet with id=60, first strand: chain 'G' and resid 537 through 540 Processing sheet with id=61, first strand: chain 'G' and resid 554 through 555 removed outlier: 4.439A pdb=" N PHE G 583 " --> pdb=" O ILE G 590 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'H' and resid 532 through 533 Processing sheet with id=63, first strand: chain 'H' and resid 537 through 540 Processing sheet with id=64, first strand: chain 'H' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE H 583 " --> pdb=" O ILE H 590 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'H' and resid 637 through 640 Processing sheet with id=66, first strand: chain 'H' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE H 649 " --> pdb=" O ASN H 750 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR H 728 " --> pdb=" O TRP H 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP H 675 " --> pdb=" O TYR H 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG H 730 " --> pdb=" O LEU H 673 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU H 673 " --> pdb=" O ARG H 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU H 732 " --> pdb=" O THR H 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR H 671 " --> pdb=" O LEU H 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL H 734 " --> pdb=" O TYR H 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 698 " --> pdb=" O LEU H 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP H 675 " --> pdb=" O GLN H 696 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN H 696 " --> pdb=" O TRP H 675 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'H' and resid 764 through 768 Processing sheet with id=68, first strand: chain 'H' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA H 836 " --> pdb=" O LEU H 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER H 888 " --> pdb=" O VAL H 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL H 834 " --> pdb=" O SER H 888 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN H 927 " --> pdb=" O ARG H 839 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'I' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE I 138 " --> pdb=" O THR I 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR I 158 " --> pdb=" O ILE I 138 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'I' and resid 146 through 148 removed outlier: 6.594A pdb=" N ALA I 147 " --> pdb=" O LYS I 219 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'I' and resid 230 through 232 Processing sheet with id=72, first strand: chain 'I' and resid 252 through 260 removed outlier: 25.580A pdb=" N GLY I 268 " --> pdb=" O VAL I 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR I 354 " --> pdb=" O GLY I 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL I 270 " --> pdb=" O TYR I 354 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE I 272 " --> pdb=" O PRO I 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG I 315 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU I 294 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL I 313 " --> pdb=" O LEU I 294 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'I' and resid 369 through 373 Processing sheet with id=74, first strand: chain 'I' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR I 391 " --> pdb=" O ARG I 525 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'I' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR I 391 " --> pdb=" O ARG I 525 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'I' and resid 532 through 533 Processing sheet with id=77, first strand: chain 'I' and resid 537 through 540 Processing sheet with id=78, first strand: chain 'I' and resid 554 through 555 removed outlier: 4.438A pdb=" N PHE I 583 " --> pdb=" O ILE I 590 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain 'J' and resid 532 through 533 Processing sheet with id=80, first strand: chain 'J' and resid 537 through 540 Processing sheet with id=81, first strand: chain 'J' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE J 583 " --> pdb=" O ILE J 590 " (cutoff:3.500A) Processing sheet with id=82, first strand: chain 'J' and resid 637 through 640 Processing sheet with id=83, first strand: chain 'J' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE J 649 " --> pdb=" O ASN J 750 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR J 728 " --> pdb=" O TRP J 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP J 675 " --> pdb=" O TYR J 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG J 730 " --> pdb=" O LEU J 673 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU J 673 " --> pdb=" O ARG J 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU J 732 " --> pdb=" O THR J 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR J 671 " --> pdb=" O LEU J 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL J 734 " --> pdb=" O TYR J 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA J 698 " --> pdb=" O LEU J 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP J 675 " --> pdb=" O GLN J 696 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN J 696 " --> pdb=" O TRP J 675 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'J' and resid 764 through 768 Processing sheet with id=85, first strand: chain 'J' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA J 836 " --> pdb=" O LEU J 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER J 888 " --> pdb=" O VAL J 834 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL J 834 " --> pdb=" O SER J 888 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN J 927 " --> pdb=" O ARG J 839 " (cutoff:3.500A) Processing sheet with id=86, first strand: chain 'K' and resid 136 through 140 removed outlier: 5.481A pdb=" N ILE K 138 " --> pdb=" O THR K 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR K 158 " --> pdb=" O ILE K 138 " (cutoff:3.500A) Processing sheet with id=87, first strand: chain 'K' and resid 146 through 148 removed outlier: 6.595A pdb=" N ALA K 147 " --> pdb=" O LYS K 219 " (cutoff:3.500A) Processing sheet with id=88, first strand: chain 'K' and resid 230 through 232 Processing sheet with id=89, first strand: chain 'K' and resid 252 through 260 removed outlier: 25.579A pdb=" N GLY K 268 " --> pdb=" O VAL K 352 " (cutoff:3.500A) removed outlier: 19.263A pdb=" N TYR K 354 " --> pdb=" O GLY K 268 " (cutoff:3.500A) removed outlier: 14.543A pdb=" N VAL K 270 " --> pdb=" O TYR K 354 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE K 272 " --> pdb=" O PRO K 356 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG K 315 " --> pdb=" O VAL K 292 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU K 294 " --> pdb=" O VAL K 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL K 313 " --> pdb=" O LEU K 294 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain 'K' and resid 369 through 373 Processing sheet with id=91, first strand: chain 'K' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR K 391 " --> pdb=" O ARG K 525 " (cutoff:3.500A) Processing sheet with id=92, first strand: chain 'K' and resid 380 through 382 removed outlier: 6.281A pdb=" N THR K 391 " --> pdb=" O ARG K 525 " (cutoff:3.500A) Processing sheet with id=93, first strand: chain 'K' and resid 532 through 533 Processing sheet with id=94, first strand: chain 'K' and resid 537 through 540 Processing sheet with id=95, first strand: chain 'K' and resid 554 through 555 removed outlier: 4.439A pdb=" N PHE K 583 " --> pdb=" O ILE K 590 " (cutoff:3.500A) Processing sheet with id=96, first strand: chain 'L' and resid 532 through 533 Processing sheet with id=97, first strand: chain 'L' and resid 537 through 540 Processing sheet with id=98, first strand: chain 'L' and resid 554 through 555 removed outlier: 4.386A pdb=" N PHE L 583 " --> pdb=" O ILE L 590 " (cutoff:3.500A) Processing sheet with id=99, first strand: chain 'L' and resid 637 through 640 Processing sheet with id=100, first strand: chain 'L' and resid 648 through 650 removed outlier: 6.296A pdb=" N PHE L 649 " --> pdb=" O ASN L 750 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR L 728 " --> pdb=" O TRP L 675 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP L 675 " --> pdb=" O TYR L 728 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG L 730 " --> pdb=" O LEU L 673 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU L 673 " --> pdb=" O ARG L 730 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU L 732 " --> pdb=" O THR L 671 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR L 671 " --> pdb=" O LEU L 732 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL L 734 " --> pdb=" O TYR L 669 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA L 698 " --> pdb=" O LEU L 673 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP L 675 " --> pdb=" O GLN L 696 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN L 696 " --> pdb=" O TRP L 675 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'L' and resid 764 through 768 Processing sheet with id=102, first strand: chain 'L' and resid 883 through 888 removed outlier: 6.619A pdb=" N ALA L 836 " --> pdb=" O LEU L 886 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER L 888 " --> pdb=" O VAL L 834 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL L 834 " --> pdb=" O SER L 888 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN L 927 " --> pdb=" O ARG L 839 " (cutoff:3.500A) 1356 hydrogen bonds defined for protein. 3384 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: 12.37 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11813 1.34 - 1.46: 11658 1.46 - 1.58: 17923 1.58 - 1.70: 0 1.70 - 1.83: 66 Bond restraints: 41460 Sorted by residual: bond pdb=" C CYS J 666 " pdb=" N GLY J 667 " ideal model delta sigma weight residual 1.325 1.351 -0.026 9.40e-03 1.13e+04 7.50e+00 bond pdb=" C CYS D 666 " pdb=" N GLY D 667 " ideal model delta sigma weight residual 1.325 1.351 -0.026 9.40e-03 1.13e+04 7.50e+00 bond pdb=" C CYS L 666 " pdb=" N GLY L 667 " ideal model delta sigma weight residual 1.325 1.350 -0.025 9.40e-03 1.13e+04 7.24e+00 bond pdb=" C CYS F 666 " pdb=" N GLY F 667 " ideal model delta sigma weight residual 1.325 1.350 -0.025 9.40e-03 1.13e+04 7.24e+00 bond pdb=" C CYS B 666 " pdb=" N GLY B 667 " ideal model delta sigma weight residual 1.325 1.350 -0.025 9.40e-03 1.13e+04 7.17e+00 ... (remaining 41455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 51236 1.56 - 3.12: 4963 3.12 - 4.68: 357 4.68 - 6.23: 36 6.23 - 7.79: 18 Bond angle restraints: 56610 Sorted by residual: angle pdb=" C PHE A 428 " pdb=" CA PHE A 428 " pdb=" CB PHE A 428 " ideal model delta sigma weight residual 109.71 101.92 7.79 1.39e+00 5.18e-01 3.14e+01 angle pdb=" C PHE G 428 " pdb=" CA PHE G 428 " pdb=" CB PHE G 428 " ideal model delta sigma weight residual 109.71 101.92 7.79 1.39e+00 5.18e-01 3.14e+01 angle pdb=" C PHE K 428 " pdb=" CA PHE K 428 " pdb=" CB PHE K 428 " ideal model delta sigma weight residual 109.71 101.94 7.77 1.39e+00 5.18e-01 3.12e+01 angle pdb=" C PHE C 428 " pdb=" CA PHE C 428 " pdb=" CB PHE C 428 " ideal model delta sigma weight residual 109.71 101.94 7.77 1.39e+00 5.18e-01 3.12e+01 angle pdb=" C PHE I 428 " pdb=" CA PHE I 428 " pdb=" CB PHE I 428 " ideal model delta sigma weight residual 109.71 101.94 7.77 1.39e+00 5.18e-01 3.12e+01 ... (remaining 56605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 22142 17.67 - 35.34: 1798 35.34 - 53.01: 414 53.01 - 70.68: 78 70.68 - 88.35: 78 Dihedral angle restraints: 24510 sinusoidal: 9030 harmonic: 15480 Sorted by residual: dihedral pdb=" CD ARG H 736 " pdb=" NE ARG H 736 " pdb=" CZ ARG H 736 " pdb=" NH1 ARG H 736 " ideal model delta sinusoidal sigma weight residual 0.00 68.65 -68.65 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CD ARG B 736 " pdb=" NE ARG B 736 " pdb=" CZ ARG B 736 " pdb=" NH1 ARG B 736 " ideal model delta sinusoidal sigma weight residual 0.00 68.65 -68.65 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CD ARG F 736 " pdb=" NE ARG F 736 " pdb=" CZ ARG F 736 " pdb=" NH1 ARG F 736 " ideal model delta sinusoidal sigma weight residual 0.00 68.64 -68.64 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 24507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3796 0.060 - 0.120: 2476 0.120 - 0.180: 310 0.180 - 0.240: 18 0.240 - 0.300: 6 Chirality restraints: 6606 Sorted by residual: chirality pdb=" CA CYS J 666 " pdb=" N CYS J 666 " pdb=" C CYS J 666 " pdb=" CB CYS J 666 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA CYS D 666 " pdb=" N CYS D 666 " pdb=" C CYS D 666 " pdb=" CB CYS D 666 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA CYS L 666 " pdb=" N CYS L 666 " pdb=" C CYS L 666 " pdb=" CB CYS L 666 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 6603 not shown) Planarity restraints: 7620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 736 " -0.902 9.50e-02 1.11e+02 4.05e-01 1.10e+02 pdb=" NE ARG F 736 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG F 736 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG F 736 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG F 736 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 736 " 0.902 9.50e-02 1.11e+02 4.05e-01 1.10e+02 pdb=" NE ARG L 736 " -0.074 2.00e-02 2.50e+03 pdb=" CZ ARG L 736 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG L 736 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG L 736 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 736 " -0.902 9.50e-02 1.11e+02 4.05e-01 1.10e+02 pdb=" NE ARG B 736 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 736 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG B 736 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 736 " -0.004 2.00e-02 2.50e+03 ... (remaining 7617 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7490 2.78 - 3.31: 38662 3.31 - 3.84: 69262 3.84 - 4.37: 85789 4.37 - 4.90: 143658 Nonbonded interactions: 344861 Sorted by model distance: nonbonded pdb=" O PRO C 415 " pdb=" OG SER C 418 " model vdw 2.250 3.040 nonbonded pdb=" O PRO I 415 " pdb=" OG SER I 418 " model vdw 2.250 3.040 nonbonded pdb=" O PRO E 415 " pdb=" OG SER E 418 " model vdw 2.250 3.040 nonbonded pdb=" O PRO K 415 " pdb=" OG SER K 418 " model vdw 2.250 3.040 nonbonded pdb=" O PRO A 415 " pdb=" OG SER A 418 " model vdw 2.250 3.040 ... (remaining 344856 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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=1.00 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: 5.180 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: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 38.960 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.080 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.007 0.044 41472 Z= 0.466 Angle : 0.950 7.792 56634 Z= 0.616 Chirality : 0.067 0.300 6606 Planarity : 0.018 0.405 7620 Dihedral : 14.995 88.346 14622 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.27 % Allowed : 15.40 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: 0.36 (0.11), residues: 5460 helix: -0.02 (0.33), residues: 288 sheet: 1.20 (0.11), residues: 1788 loop : -0.25 (0.10), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.004 ARG L 736 TYR 0.037 0.005 TYR J 837 PHE 0.026 0.006 PHE B 900 TRP 0.022 0.006 TRP D 877 HIS 0.009 0.006 HIS L 693 Details of bonding type rmsd covalent geometry : bond 0.00729 (41460) covalent geometry : angle 0.94843 (56610) SS BOND : bond 0.03114 ( 12) SS BOND : angle 2.95222 ( 24) hydrogen bonds : bond 0.11389 ( 1308) hydrogen bonds : angle 6.30037 ( 3384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 1.270 Fit side-chains REVERT: A 179 GLN cc_start: 0.4788 (tm-30) cc_final: 0.4549 (tm130) REVERT: B 776 MET cc_start: 0.7718 (ptt) cc_final: 0.7439 (ptt) REVERT: D 645 MET cc_start: 0.8039 (mtp) cc_final: 0.7829 (mmm) REVERT: F 947 GLN cc_start: 0.8200 (tp40) cc_final: 0.7958 (mm-40) REVERT: G 179 GLN cc_start: 0.4782 (tm-30) cc_final: 0.4543 (tm130) REVERT: H 776 MET cc_start: 0.7717 (ptt) cc_final: 0.7437 (ptt) REVERT: J 645 MET cc_start: 0.8038 (mtp) cc_final: 0.7829 (mmm) REVERT: L 947 GLN cc_start: 0.8203 (tp40) cc_final: 0.7961 (mm-40) outliers start: 12 outliers final: 0 residues processed: 226 average time/residue: 0.6889 time to fit residues: 192.5514 Evaluate side-chains 146 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 394 optimal weight: 0.3980 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 0.5980 chunk 366 optimal weight: 30.0000 chunk 223 optimal weight: 7.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 780 ASN B 876 ASN C 380 ASN C 422 GLN D 780 ASN D 846 ASN D 876 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN F 780 ASN F 876 ASN G 422 GLN H 569 ASN H 780 ASN H 876 ASN I 380 ASN I 422 GLN J 780 ASN J 846 ASN J 876 ASN ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN L 780 ASN L 876 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.113918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.087620 restraints weight = 69632.495| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.49 r_work: 0.3398 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 41472 Z= 0.149 Angle : 0.556 8.343 56634 Z= 0.298 Chirality : 0.046 0.195 6606 Planarity : 0.004 0.043 7620 Dihedral : 4.804 27.925 5898 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.23 % Allowed : 14.26 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: 0.25 (0.11), residues: 5460 helix: -0.29 (0.31), residues: 288 sheet: 1.09 (0.11), residues: 1806 loop : -0.29 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 509 TYR 0.012 0.002 TYR H 837 PHE 0.016 0.002 PHE H 840 TRP 0.011 0.002 TRP F 675 HIS 0.006 0.003 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.00342 (41460) covalent geometry : angle 0.55468 (56610) SS BOND : bond 0.01574 ( 12) SS BOND : angle 1.65507 ( 24) hydrogen bonds : bond 0.03315 ( 1308) hydrogen bonds : angle 5.21479 ( 3384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 166 time to evaluate : 1.655 Fit side-chains REVERT: A 422 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: A 588 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7745 (mtp180) REVERT: B 776 MET cc_start: 0.7879 (ptt) cc_final: 0.7640 (ptt) REVERT: C 250 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: D 890 ASP cc_start: 0.4944 (m-30) cc_final: 0.4330 (m-30) REVERT: F 839 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7878 (ttp-170) REVERT: F 947 GLN cc_start: 0.8106 (tp40) cc_final: 0.7828 (mm-40) REVERT: G 422 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: G 588 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7743 (mtp180) REVERT: H 776 MET cc_start: 0.7878 (ptt) cc_final: 0.7637 (ptt) REVERT: I 250 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: J 890 ASP cc_start: 0.4934 (m-30) cc_final: 0.4328 (m-30) REVERT: L 839 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7879 (ttp-170) REVERT: L 947 GLN cc_start: 0.8105 (tp40) cc_final: 0.7833 (mm-40) outliers start: 98 outliers final: 58 residues processed: 260 average time/residue: 0.6546 time to fit residues: 215.4743 Evaluate side-chains 192 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 128 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 839 ARG Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 561 ILE Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 250 ASP Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 686 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 422 GLN Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 597 THR Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 839 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 387 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 399 optimal weight: 9.9990 chunk 390 optimal weight: 3.9990 chunk 276 optimal weight: 40.0000 chunk 64 optimal weight: 7.9990 chunk 92 optimal weight: 40.0000 chunk 495 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 380 ASN A 422 GLN A 499 ASN B 569 ASN B 598 ASN B 846 ASN C 422 GLN C 499 ASN D 569 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 499 ASN F 569 ASN F 598 ASN F 646 GLN F 719 GLN F 846 ASN G 305 ASN G 380 ASN G 422 GLN G 499 ASN H 598 ASN H 846 ASN I 422 GLN I 499 ASN I 594 GLN J 569 ASN ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN K 499 ASN L 569 ASN L 598 ASN L 646 GLN L 719 GLN L 846 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.113494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.087545 restraints weight = 67418.491| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.87 r_work: 0.3301 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 41472 Z= 0.314 Angle : 0.697 8.789 56634 Z= 0.377 Chirality : 0.052 0.174 6606 Planarity : 0.005 0.051 7620 Dihedral : 5.620 40.977 5898 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.13 % Allowed : 13.53 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.22 (0.10), residues: 5460 helix: -0.67 (0.29), residues: 288 sheet: 0.92 (0.11), residues: 1836 loop : -0.73 (0.10), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 509 TYR 0.023 0.003 TYR B 837 PHE 0.028 0.003 PHE H 840 TRP 0.014 0.003 TRP L 675 HIS 0.007 0.004 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.00744 (41460) covalent geometry : angle 0.69713 (56610) SS BOND : bond 0.00764 ( 12) SS BOND : angle 0.61669 ( 24) hydrogen bonds : bond 0.04378 ( 1308) hydrogen bonds : angle 5.80620 ( 3384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 128 time to evaluate : 1.624 Fit side-chains REVERT: A 422 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8147 (pm20) REVERT: B 776 MET cc_start: 0.7995 (ptt) cc_final: 0.7741 (ptt) REVERT: C 183 THR cc_start: 0.5607 (p) cc_final: 0.5396 (m) REVERT: D 839 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7541 (ttt180) REVERT: D 890 ASP cc_start: 0.5704 (m-30) cc_final: 0.5027 (m-30) REVERT: E 422 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: G 422 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8144 (pm20) REVERT: H 776 MET cc_start: 0.7992 (ptt) cc_final: 0.7741 (ptt) REVERT: I 183 THR cc_start: 0.5612 (p) cc_final: 0.5397 (m) REVERT: J 839 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7536 (ttt180) REVERT: J 890 ASP cc_start: 0.5698 (m-30) cc_final: 0.5015 (m-30) REVERT: K 422 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8208 (pm20) outliers start: 138 outliers final: 82 residues processed: 260 average time/residue: 0.6371 time to fit residues: 210.6899 Evaluate side-chains 216 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 128 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 891 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 305 ASN Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 561 ILE Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 645 MET Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 422 GLN Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain K residue 597 THR Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 891 THR Chi-restraints excluded: chain L residue 945 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 49 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 402 optimal weight: 10.0000 chunk 516 optimal weight: 7.9990 chunk 513 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 449 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 412 optimal weight: 0.9980 chunk 361 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 422 GLN A 528 ASN C 422 GLN E 422 GLN E 599 GLN G 305 ASN G 422 GLN G 528 ASN I 422 GLN K 422 GLN K 599 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.114142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087869 restraints weight = 67770.442| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.79 r_work: 0.3342 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41472 Z= 0.140 Angle : 0.550 9.051 56634 Z= 0.294 Chirality : 0.045 0.163 6606 Planarity : 0.004 0.050 7620 Dihedral : 5.098 37.379 5898 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.72 % Allowed : 13.60 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.01 (0.11), residues: 5460 helix: -0.13 (0.31), residues: 288 sheet: 0.98 (0.11), residues: 1836 loop : -0.57 (0.10), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 509 TYR 0.012 0.001 TYR K 502 PHE 0.015 0.002 PHE B 840 TRP 0.014 0.002 TRP L 675 HIS 0.005 0.002 HIS H 693 Details of bonding type rmsd covalent geometry : bond 0.00323 (41460) covalent geometry : angle 0.55043 (56610) SS BOND : bond 0.00339 ( 12) SS BOND : angle 0.45379 ( 24) hydrogen bonds : bond 0.03323 ( 1308) hydrogen bonds : angle 5.36379 ( 3384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 146 time to evaluate : 1.568 Fit side-chains REVERT: A 226 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8241 (mtp180) REVERT: B 776 MET cc_start: 0.7876 (ptt) cc_final: 0.7676 (ptt) REVERT: B 860 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7786 (mtp180) REVERT: C 226 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8226 (mtp180) REVERT: C 422 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: D 839 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7380 (ttt180) REVERT: D 890 ASP cc_start: 0.5638 (m-30) cc_final: 0.5012 (m-30) REVERT: D 945 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8748 (t) REVERT: G 226 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8239 (mtp180) REVERT: H 776 MET cc_start: 0.7872 (ptt) cc_final: 0.7670 (ptt) REVERT: H 860 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7785 (mtp180) REVERT: I 226 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8236 (mtp180) REVERT: I 422 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8442 (pm20) REVERT: J 839 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7380 (ttt180) REVERT: J 890 ASP cc_start: 0.5630 (m-30) cc_final: 0.5016 (m-30) REVERT: J 945 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8749 (t) outliers start: 120 outliers final: 74 residues processed: 258 average time/residue: 0.6973 time to fit residues: 225.5239 Evaluate side-chains 211 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 125 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 628 LYS Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 891 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 305 ASN Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 686 THR Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 860 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain I residue 422 GLN Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain K residue 597 THR Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 891 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 191 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 515 optimal weight: 9.9990 chunk 322 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 189 optimal weight: 40.0000 chunk 456 optimal weight: 30.0000 chunk 121 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 422 GLN C 422 GLN C 594 GLN E 422 GLN E 599 GLN G 305 ASN G 422 GLN I 422 GLN K 422 GLN K 599 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.114140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086723 restraints weight = 68814.746| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.51 r_work: 0.3309 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 41472 Z= 0.299 Angle : 0.679 9.515 56634 Z= 0.365 Chirality : 0.051 0.170 6606 Planarity : 0.005 0.053 7620 Dihedral : 5.642 40.907 5898 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.00 % Allowed : 14.62 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.40 (0.10), residues: 5460 helix: -0.57 (0.30), residues: 288 sheet: 0.83 (0.11), residues: 1836 loop : -0.90 (0.10), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 509 TYR 0.021 0.003 TYR L 837 PHE 0.025 0.003 PHE D 840 TRP 0.014 0.003 TRP L 675 HIS 0.007 0.004 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.00706 (41460) covalent geometry : angle 0.67849 (56610) SS BOND : bond 0.00568 ( 12) SS BOND : angle 0.79232 ( 24) hydrogen bonds : bond 0.04236 ( 1308) hydrogen bonds : angle 5.84436 ( 3384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 126 time to evaluate : 1.675 Fit side-chains REVERT: A 226 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8365 (mtp180) REVERT: A 448 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6785 (tt0) REVERT: B 776 MET cc_start: 0.7939 (ptt) cc_final: 0.7693 (ptt) REVERT: B 860 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7762 (mtp180) REVERT: C 183 THR cc_start: 0.5711 (p) cc_final: 0.5497 (m) REVERT: C 226 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8247 (mtp180) REVERT: C 422 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: D 839 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7494 (ttt180) REVERT: D 890 ASP cc_start: 0.5591 (m-30) cc_final: 0.5037 (m-30) REVERT: D 945 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8713 (t) REVERT: E 422 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: E 554 CYS cc_start: 0.6947 (t) cc_final: 0.6570 (m) REVERT: E 555 LEU cc_start: 0.8132 (tt) cc_final: 0.7899 (tt) REVERT: G 226 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8359 (mtp180) REVERT: G 448 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: H 776 MET cc_start: 0.7934 (ptt) cc_final: 0.7690 (ptt) REVERT: H 860 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7760 (mtp180) REVERT: I 183 THR cc_start: 0.5710 (p) cc_final: 0.5493 (m) REVERT: I 226 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8253 (mtp180) REVERT: I 422 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: J 839 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7495 (ttt180) REVERT: J 890 ASP cc_start: 0.5589 (m-30) cc_final: 0.5036 (m-30) REVERT: J 945 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8716 (t) REVERT: K 422 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: K 554 CYS cc_start: 0.6950 (t) cc_final: 0.6571 (m) REVERT: K 555 LEU cc_start: 0.8131 (tt) cc_final: 0.7902 (tt) outliers start: 132 outliers final: 98 residues processed: 248 average time/residue: 0.6558 time to fit residues: 206.6491 Evaluate side-chains 238 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 124 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain F residue 533 ILE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 628 LYS Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 891 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 305 ASN Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 561 ILE Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 625 THR Chi-restraints excluded: chain H residue 686 THR Chi-restraints excluded: chain H residue 743 SER Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 860 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 422 GLN Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 422 GLN Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain L residue 533 ILE Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 891 THR Chi-restraints excluded: chain L residue 945 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 142 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 520 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 269 optimal weight: 0.8980 chunk 401 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 422 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN E 380 ASN E 422 GLN E 599 GLN G 305 ASN G 422 GLN ** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN K 422 GLN K 599 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.116125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088815 restraints weight = 68750.577| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.51 r_work: 0.3357 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 41472 Z= 0.127 Angle : 0.536 9.645 56634 Z= 0.288 Chirality : 0.045 0.161 6606 Planarity : 0.004 0.050 7620 Dihedral : 5.061 36.147 5898 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.72 % Allowed : 14.78 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.12 (0.11), residues: 5460 helix: -0.08 (0.31), residues: 288 sheet: 0.95 (0.11), residues: 1836 loop : -0.69 (0.10), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 758 TYR 0.011 0.001 TYR I 502 PHE 0.012 0.002 PHE B 840 TRP 0.015 0.001 TRP F 675 HIS 0.004 0.002 HIS H 693 Details of bonding type rmsd covalent geometry : bond 0.00288 (41460) covalent geometry : angle 0.53576 (56610) SS BOND : bond 0.00302 ( 12) SS BOND : angle 0.51861 ( 24) hydrogen bonds : bond 0.03157 ( 1308) hydrogen bonds : angle 5.32059 ( 3384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 144 time to evaluate : 1.690 Fit side-chains REVERT: A 226 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8004 (mtp85) REVERT: A 422 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: A 509 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6620 (ptm-80) REVERT: B 776 MET cc_start: 0.7881 (ptt) cc_final: 0.7659 (ptt) REVERT: B 860 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7766 (mtp180) REVERT: C 183 THR cc_start: 0.5716 (p) cc_final: 0.5487 (m) REVERT: C 226 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8230 (mtp180) REVERT: D 839 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7318 (ttt180) REVERT: D 890 ASP cc_start: 0.5683 (m-30) cc_final: 0.5184 (m-30) REVERT: D 945 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8753 (t) REVERT: E 422 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: E 554 CYS cc_start: 0.6879 (t) cc_final: 0.6528 (m) REVERT: E 555 LEU cc_start: 0.8210 (tt) cc_final: 0.7994 (tt) REVERT: G 226 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8010 (mtp85) REVERT: G 422 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: G 509 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.6625 (ptm-80) REVERT: H 776 MET cc_start: 0.7872 (ptt) cc_final: 0.7649 (ptt) REVERT: H 860 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7764 (mtp180) REVERT: I 183 THR cc_start: 0.5714 (p) cc_final: 0.5484 (m) REVERT: I 226 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8230 (mtp180) REVERT: J 839 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7333 (ttt180) REVERT: J 890 ASP cc_start: 0.5677 (m-30) cc_final: 0.5171 (m-30) REVERT: J 945 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8758 (t) REVERT: K 422 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: K 554 CYS cc_start: 0.6899 (t) cc_final: 0.6537 (m) REVERT: K 555 LEU cc_start: 0.8205 (tt) cc_final: 0.7991 (tt) outliers start: 120 outliers final: 84 residues processed: 256 average time/residue: 0.6830 time to fit residues: 220.0052 Evaluate side-chains 233 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 133 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 509 ARG Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 628 LYS Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 891 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 686 THR Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 860 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 532 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 422 GLN Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain K residue 597 THR Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 891 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 442 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 374 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 378 optimal weight: 8.9990 chunk 212 optimal weight: 0.0470 chunk 73 optimal weight: 6.9990 overall best weight: 6.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 422 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN E 422 GLN E 599 GLN G 305 ASN G 422 GLN ** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN K 422 GLN K 599 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.114417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.086857 restraints weight = 68641.710| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.52 r_work: 0.3317 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 41472 Z= 0.260 Angle : 0.641 9.000 56634 Z= 0.345 Chirality : 0.049 0.167 6606 Planarity : 0.005 0.051 7620 Dihedral : 5.499 38.855 5898 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.07 % Allowed : 15.08 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.43 (0.10), residues: 5460 helix: -0.76 (0.29), residues: 324 sheet: 0.79 (0.11), residues: 1848 loop : -0.90 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 509 TYR 0.017 0.002 TYR L 837 PHE 0.023 0.003 PHE J 840 TRP 0.013 0.002 TRP L 675 HIS 0.006 0.004 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.00613 (41460) covalent geometry : angle 0.64140 (56610) SS BOND : bond 0.00487 ( 12) SS BOND : angle 0.80871 ( 24) hydrogen bonds : bond 0.03976 ( 1308) hydrogen bonds : angle 5.70066 ( 3384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 132 time to evaluate : 1.642 Fit side-chains REVERT: A 183 THR cc_start: 0.5993 (p) cc_final: 0.5791 (m) REVERT: A 226 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8312 (mtp180) REVERT: A 509 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8080 (ptm-80) REVERT: B 776 MET cc_start: 0.7897 (ptt) cc_final: 0.7654 (ptt) REVERT: B 860 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7751 (mtp180) REVERT: C 183 THR cc_start: 0.5709 (p) cc_final: 0.5502 (m) REVERT: C 226 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8283 (mtp180) REVERT: D 839 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7454 (ttt180) REVERT: D 890 ASP cc_start: 0.5706 (m-30) cc_final: 0.5193 (m-30) REVERT: D 945 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8708 (t) REVERT: E 226 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8304 (mtp180) REVERT: E 422 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: E 554 CYS cc_start: 0.6795 (t) cc_final: 0.6416 (m) REVERT: G 183 THR cc_start: 0.5999 (p) cc_final: 0.5798 (m) REVERT: G 226 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8307 (mtp180) REVERT: G 509 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8168 (ptm-80) REVERT: H 776 MET cc_start: 0.7896 (ptt) cc_final: 0.7652 (ptt) REVERT: H 860 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7747 (mtp180) REVERT: I 183 THR cc_start: 0.5708 (p) cc_final: 0.5495 (m) REVERT: I 226 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8302 (mtp180) REVERT: J 839 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7438 (ttt180) REVERT: J 890 ASP cc_start: 0.5701 (m-30) cc_final: 0.5195 (m-30) REVERT: J 945 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8712 (t) REVERT: K 226 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8294 (mtp180) REVERT: K 422 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: K 554 CYS cc_start: 0.6731 (t) cc_final: 0.6349 (m) outliers start: 135 outliers final: 99 residues processed: 257 average time/residue: 0.6683 time to fit residues: 216.4034 Evaluate side-chains 242 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 127 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 558 ILE Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain F residue 533 ILE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 891 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain F residue 948 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 305 ASN Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 686 THR Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 860 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 558 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 532 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 ARG Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 422 GLN Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain L residue 533 ILE Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 891 THR Chi-restraints excluded: chain L residue 945 THR Chi-restraints excluded: chain L residue 948 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 252 optimal weight: 0.9980 chunk 402 optimal weight: 10.0000 chunk 277 optimal weight: 50.0000 chunk 420 optimal weight: 8.9990 chunk 446 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 285 optimal weight: 0.9990 chunk 236 optimal weight: 8.9990 chunk 411 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN E 422 GLN E 599 GLN G 422 GLN ** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 GLN K 422 GLN K 599 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.114896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087633 restraints weight = 68526.471| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.49 r_work: 0.3337 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 41472 Z= 0.180 Angle : 0.584 12.841 56634 Z= 0.312 Chirality : 0.047 0.200 6606 Planarity : 0.004 0.051 7620 Dihedral : 5.306 37.674 5898 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.84 % Allowed : 15.37 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.33 (0.11), residues: 5460 helix: -0.60 (0.29), residues: 324 sheet: 0.83 (0.11), residues: 1848 loop : -0.82 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 394 TYR 0.013 0.002 TYR A 502 PHE 0.017 0.002 PHE B 840 TRP 0.015 0.002 TRP F 675 HIS 0.006 0.003 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.00420 (41460) covalent geometry : angle 0.58437 (56610) SS BOND : bond 0.00367 ( 12) SS BOND : angle 0.65824 ( 24) hydrogen bonds : bond 0.03511 ( 1308) hydrogen bonds : angle 5.50636 ( 3384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 134 time to evaluate : 1.332 Fit side-chains REVERT: A 183 THR cc_start: 0.5961 (p) cc_final: 0.5755 (m) REVERT: A 226 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8113 (mtp180) REVERT: A 422 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: A 509 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6903 (ptm-80) REVERT: B 776 MET cc_start: 0.7877 (ptt) cc_final: 0.7653 (ptt) REVERT: B 860 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7781 (mtp180) REVERT: C 183 THR cc_start: 0.5718 (p) cc_final: 0.5500 (m) REVERT: C 226 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8200 (mtp180) REVERT: D 839 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7376 (ttt180) REVERT: D 890 ASP cc_start: 0.5672 (m-30) cc_final: 0.5186 (m-30) REVERT: D 945 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8706 (t) REVERT: E 226 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8255 (mtp85) REVERT: E 554 CYS cc_start: 0.6760 (t) cc_final: 0.6337 (m) REVERT: G 183 THR cc_start: 0.5963 (p) cc_final: 0.5757 (m) REVERT: G 226 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8120 (mtp180) REVERT: G 422 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8249 (pm20) REVERT: G 509 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.6907 (ptm-80) REVERT: H 776 MET cc_start: 0.7873 (ptt) cc_final: 0.7645 (ptt) REVERT: H 860 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7786 (mtp180) REVERT: I 183 THR cc_start: 0.5718 (p) cc_final: 0.5499 (m) REVERT: I 226 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8196 (mtp180) REVERT: J 839 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7373 (ttt180) REVERT: J 890 ASP cc_start: 0.5670 (m-30) cc_final: 0.5187 (m-30) REVERT: J 945 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8706 (t) REVERT: K 226 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8251 (mtp85) REVERT: K 554 CYS cc_start: 0.6782 (t) cc_final: 0.6344 (m) outliers start: 125 outliers final: 93 residues processed: 249 average time/residue: 0.5843 time to fit residues: 183.8778 Evaluate side-chains 239 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 130 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain F residue 533 ILE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 891 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain F residue 948 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 561 ILE Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 686 THR Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 860 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 ARG Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain L residue 533 ILE Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 606 THR Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 891 THR Chi-restraints excluded: chain L residue 945 THR Chi-restraints excluded: chain L residue 948 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 3 optimal weight: 40.0000 chunk 113 optimal weight: 3.9990 chunk 397 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 328 optimal weight: 9.9990 chunk 142 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 545 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN C 422 GLN E 422 GLN E 599 GLN G 422 GLN I 422 GLN K 380 ASN K 422 GLN K 599 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.115290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.087989 restraints weight = 68812.342| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.51 r_work: 0.3350 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41472 Z= 0.147 Angle : 0.552 11.915 56634 Z= 0.295 Chirality : 0.045 0.191 6606 Planarity : 0.004 0.050 7620 Dihedral : 5.101 35.907 5898 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.52 % Allowed : 15.69 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.19 (0.11), residues: 5460 helix: -0.09 (0.31), residues: 288 sheet: 0.92 (0.11), residues: 1836 loop : -0.75 (0.10), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 423 TYR 0.012 0.001 TYR I 502 PHE 0.014 0.002 PHE B 840 TRP 0.015 0.002 TRP F 675 HIS 0.005 0.003 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.00338 (41460) covalent geometry : angle 0.55238 (56610) SS BOND : bond 0.00327 ( 12) SS BOND : angle 0.66187 ( 24) hydrogen bonds : bond 0.03242 ( 1308) hydrogen bonds : angle 5.31654 ( 3384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 137 time to evaluate : 1.267 Fit side-chains REVERT: A 226 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8184 (mtp85) REVERT: A 509 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.6679 (ptm-80) REVERT: B 776 MET cc_start: 0.7878 (ptt) cc_final: 0.7653 (ptt) REVERT: B 860 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7771 (mtp180) REVERT: C 183 THR cc_start: 0.5720 (p) cc_final: 0.5497 (m) REVERT: C 226 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8224 (mtp180) REVERT: D 839 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7356 (ttt180) REVERT: D 890 ASP cc_start: 0.5631 (m-30) cc_final: 0.5152 (m-30) REVERT: D 945 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8746 (t) REVERT: E 134 PHE cc_start: 0.5021 (p90) cc_final: 0.4316 (p90) REVERT: E 226 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8237 (mtp85) REVERT: E 422 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: E 554 CYS cc_start: 0.6844 (t) cc_final: 0.6390 (m) REVERT: G 226 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8193 (mtp85) REVERT: G 509 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.6683 (ptm-80) REVERT: H 776 MET cc_start: 0.7874 (ptt) cc_final: 0.7646 (ptt) REVERT: H 860 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7770 (mtp180) REVERT: I 183 THR cc_start: 0.5712 (p) cc_final: 0.5488 (m) REVERT: I 226 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8219 (mtp180) REVERT: J 839 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7355 (ttt180) REVERT: J 890 ASP cc_start: 0.5626 (m-30) cc_final: 0.5151 (m-30) REVERT: J 945 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8746 (t) REVERT: K 134 PHE cc_start: 0.5026 (p90) cc_final: 0.4316 (p90) REVERT: K 226 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8230 (mtp85) REVERT: K 422 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: K 554 CYS cc_start: 0.6858 (t) cc_final: 0.6394 (m) outliers start: 111 outliers final: 89 residues processed: 240 average time/residue: 0.5831 time to fit residues: 176.6539 Evaluate side-chains 237 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 132 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 891 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 625 THR Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 860 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 ARG Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 422 GLN Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 606 THR Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 891 THR Chi-restraints excluded: chain L residue 945 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 249 optimal weight: 9.9990 chunk 319 optimal weight: 0.8980 chunk 371 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 chunk 308 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 519 optimal weight: 4.9990 chunk 534 optimal weight: 4.9990 chunk 454 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 422 GLN C 422 GLN E 422 GLN E 599 GLN G 305 ASN G 422 GLN I 422 GLN K 422 GLN K 599 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.115088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.087828 restraints weight = 68376.098| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.50 r_work: 0.3336 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 41472 Z= 0.200 Angle : 0.592 11.412 56634 Z= 0.317 Chirality : 0.047 0.188 6606 Planarity : 0.004 0.050 7620 Dihedral : 5.258 36.453 5898 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.68 % Allowed : 15.58 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.32 (0.11), residues: 5460 helix: -0.58 (0.29), residues: 324 sheet: 0.83 (0.11), residues: 1848 loop : -0.81 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 423 TYR 0.014 0.002 TYR G 502 PHE 0.019 0.002 PHE D 840 TRP 0.013 0.002 TRP F 675 HIS 0.005 0.003 HIS H 693 Details of bonding type rmsd covalent geometry : bond 0.00467 (41460) covalent geometry : angle 0.59230 (56610) SS BOND : bond 0.00429 ( 12) SS BOND : angle 0.75231 ( 24) hydrogen bonds : bond 0.03559 ( 1308) hydrogen bonds : angle 5.46091 ( 3384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10920 Ramachandran restraints generated. 5460 Oldfield, 0 Emsley, 5460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 137 time to evaluate : 1.631 Fit side-chains REVERT: A 226 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8203 (mtp180) REVERT: A 509 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7044 (ptm-80) REVERT: B 776 MET cc_start: 0.7887 (ptt) cc_final: 0.7656 (ptt) REVERT: B 860 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7763 (mtp180) REVERT: C 183 THR cc_start: 0.5720 (p) cc_final: 0.5514 (m) REVERT: C 226 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8236 (mtp180) REVERT: D 839 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7380 (ttt180) REVERT: D 890 ASP cc_start: 0.5681 (m-30) cc_final: 0.5143 (m-30) REVERT: D 945 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8731 (t) REVERT: E 134 PHE cc_start: 0.5014 (p90) cc_final: 0.4298 (p90) REVERT: E 226 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8233 (mtp85) REVERT: E 422 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8042 (pm20) REVERT: E 554 CYS cc_start: 0.6918 (t) cc_final: 0.6477 (m) REVERT: G 226 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8210 (mtp180) REVERT: G 509 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7048 (ptm-80) REVERT: H 776 MET cc_start: 0.7881 (ptt) cc_final: 0.7649 (ptt) REVERT: H 860 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7764 (mtp180) REVERT: I 183 THR cc_start: 0.5718 (p) cc_final: 0.5510 (m) REVERT: I 226 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8241 (mtp180) REVERT: J 839 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7377 (ttt180) REVERT: J 890 ASP cc_start: 0.5686 (m-30) cc_final: 0.5148 (m-30) REVERT: J 945 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8732 (t) REVERT: K 134 PHE cc_start: 0.5008 (p90) cc_final: 0.4289 (p90) REVERT: K 226 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8233 (mtp85) REVERT: K 422 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: K 554 CYS cc_start: 0.6919 (t) cc_final: 0.6474 (m) outliers start: 118 outliers final: 96 residues processed: 247 average time/residue: 0.6683 time to fit residues: 208.8618 Evaluate side-chains 244 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 132 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 860 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 753 ILE Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 839 ARG Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 597 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 625 THR Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 681 VAL Chi-restraints excluded: chain F residue 707 LYS Chi-restraints excluded: chain F residue 753 ILE Chi-restraints excluded: chain F residue 790 VAL Chi-restraints excluded: chain F residue 795 THR Chi-restraints excluded: chain F residue 891 THR Chi-restraints excluded: chain F residue 945 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 305 ASN Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 597 THR Chi-restraints excluded: chain H residue 533 ILE Chi-restraints excluded: chain H residue 573 VAL Chi-restraints excluded: chain H residue 625 THR Chi-restraints excluded: chain H residue 743 SER Chi-restraints excluded: chain H residue 753 ILE Chi-restraints excluded: chain H residue 790 VAL Chi-restraints excluded: chain H residue 795 THR Chi-restraints excluded: chain H residue 860 ARG Chi-restraints excluded: chain H residue 864 VAL Chi-restraints excluded: chain H residue 945 THR Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 222 VAL Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain I residue 548 SER Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 533 ILE Chi-restraints excluded: chain J residue 573 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 634 THR Chi-restraints excluded: chain J residue 753 ILE Chi-restraints excluded: chain J residue 790 VAL Chi-restraints excluded: chain J residue 795 THR Chi-restraints excluded: chain J residue 839 ARG Chi-restraints excluded: chain J residue 945 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 222 VAL Chi-restraints excluded: chain K residue 226 ARG Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 422 GLN Chi-restraints excluded: chain K residue 548 SER Chi-restraints excluded: chain L residue 573 VAL Chi-restraints excluded: chain L residue 606 THR Chi-restraints excluded: chain L residue 625 THR Chi-restraints excluded: chain L residue 635 ASP Chi-restraints excluded: chain L residue 681 VAL Chi-restraints excluded: chain L residue 707 LYS Chi-restraints excluded: chain L residue 753 ILE Chi-restraints excluded: chain L residue 790 VAL Chi-restraints excluded: chain L residue 795 THR Chi-restraints excluded: chain L residue 891 THR Chi-restraints excluded: chain L residue 945 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 494 optimal weight: 6.9990 chunk 452 optimal weight: 9.9990 chunk 478 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 345 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 489 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 523 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN C 422 GLN E 422 GLN E 599 GLN G 422 GLN I 422 GLN K 422 GLN K 599 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.115004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.087754 restraints weight = 68752.133| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.50 r_work: 0.3334 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 41472 Z= 0.199 Angle : 0.594 11.134 56634 Z= 0.317 Chirality : 0.047 0.176 6606 Planarity : 0.004 0.050 7620 Dihedral : 5.288 36.824 5898 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.68 % Allowed : 15.55 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.11 % 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 aren not related in a simple way. whole: -0.33 (0.11), residues: 5460 helix: -0.59 (0.29), residues: 324 sheet: 0.82 (0.11), residues: 1848 loop : -0.82 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 880 TYR 0.014 0.002 TYR K 502 PHE 0.018 0.002 PHE D 840 TRP 0.013 0.002 TRP F 675 HIS 0.006 0.003 HIS H 693 Details of bonding type rmsd covalent geometry : bond 0.00464 (41460) covalent geometry : angle 0.59402 (56610) SS BOND : bond 0.00418 ( 12) SS BOND : angle 0.75082 ( 24) hydrogen bonds : bond 0.03568 ( 1308) hydrogen bonds : angle 5.47888 ( 3384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23034.28 seconds wall clock time: 391 minutes 21.95 seconds (23481.95 seconds total)