Starting phenix.real_space_refine on Sat Feb 7 12:01:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hlm_52260/02_2026/9hlm_52260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hlm_52260/02_2026/9hlm_52260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hlm_52260/02_2026/9hlm_52260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hlm_52260/02_2026/9hlm_52260.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hlm_52260/02_2026/9hlm_52260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hlm_52260/02_2026/9hlm_52260.map" } resolution = 3.7 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= 0.017 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 152 5.16 5 C 20288 2.51 5 N 5668 2.21 5 O 5932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 256 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32040 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 8010 Classifications: {'peptide': 996} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 930} Chain breaks: 4 Restraints were copied for chains: B, C, D Time building chain proxies: 10.03, per 1000 atoms: 0.31 Number of scatterers: 32040 At special positions: 0 Unit cell: (103.092, 152.46, 196.02, 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 152 16.00 O 5932 8.00 N 5668 7.00 C 20288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7424 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 64 sheets defined 17.4% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 12 through 18 removed outlier: 6.190A pdb=" N ASP A 15 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TRP A 16 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.928A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 removed outlier: 4.573A pdb=" N LEU A 426 " --> pdb=" O MET A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 448 removed outlier: 4.188A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 Processing helix chain 'A' and resid 488 through 492 removed outlier: 4.320A pdb=" N ASP A 492 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 598 through 603 removed outlier: 4.037A pdb=" N CYS A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 4.104A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 814 Processing helix chain 'A' and resid 906 through 910 removed outlier: 4.208A pdb=" N LEU A 910 " --> pdb=" O PRO A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 12 through 18 removed outlier: 6.190A pdb=" N ASP B 15 " --> pdb=" O GLN B 12 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TRP B 16 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.928A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 4.573A pdb=" N LEU B 426 " --> pdb=" O MET B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 448 removed outlier: 4.188A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 479 Processing helix chain 'B' and resid 488 through 492 removed outlier: 4.320A pdb=" N ASP B 492 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 598 through 603 removed outlier: 4.037A pdb=" N CYS B 602 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 removed outlier: 4.104A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 906 through 910 removed outlier: 4.208A pdb=" N LEU B 910 " --> pdb=" O PRO B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 12 through 18 removed outlier: 6.190A pdb=" N ASP C 15 " --> pdb=" O GLN C 12 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TRP C 16 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 368 through 381 Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.928A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 removed outlier: 4.573A pdb=" N LEU C 426 " --> pdb=" O MET C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 448 removed outlier: 4.188A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 479 Processing helix chain 'C' and resid 488 through 492 removed outlier: 4.320A pdb=" N ASP C 492 " --> pdb=" O GLY C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 598 through 603 removed outlier: 4.037A pdb=" N CYS C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 624 removed outlier: 4.104A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 814 Processing helix chain 'C' and resid 906 through 910 removed outlier: 4.208A pdb=" N LEU C 910 " --> pdb=" O PRO C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 972 through 976 Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 18 removed outlier: 6.190A pdb=" N ASP D 15 " --> pdb=" O GLN D 12 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TRP D 16 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 130 through 134 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 368 through 381 Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.928A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 426 removed outlier: 4.573A pdb=" N LEU D 426 " --> pdb=" O MET D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 448 removed outlier: 4.188A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 479 Processing helix chain 'D' and resid 488 through 492 removed outlier: 4.320A pdb=" N ASP D 492 " --> pdb=" O GLY D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 598 through 603 removed outlier: 4.037A pdb=" N CYS D 602 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 removed outlier: 4.104A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 906 through 910 removed outlier: 4.208A pdb=" N LEU D 910 " --> pdb=" O PRO D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 972 through 976 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 63 removed outlier: 3.512A pdb=" N MET A 187 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 149 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.661A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.901A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 230 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.901A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 230 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 273 removed outlier: 5.695A pdb=" N GLN A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN A 262 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 311 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 354 removed outlier: 7.262A pdb=" N LEU A 533 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 565 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU A 535 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 567 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLU A 537 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 386 through 387 removed outlier: 6.893A pdb=" N VAL A 387 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLU A 412 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP A 411 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 575 through 578 removed outlier: 3.684A pdb=" N LEU A 575 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB4, first strand: chain 'A' and resid 661 through 669 removed outlier: 6.529A pdb=" N VAL A 656 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 665 " --> pdb=" O TRP A 654 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP A 654 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU A 667 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 652 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY A 692 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA A 723 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A 694 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG A 721 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 696 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN A 719 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A 698 " --> pdb=" O TRP A 717 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP A 717 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 700 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 741 through 742 removed outlier: 3.648A pdb=" N GLN A 767 " --> pdb=" O GLN A 757 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 770 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 773 " --> pdb=" O ILE A 770 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 776 through 782 removed outlier: 5.591A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.402A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.245A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 21.079A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.454A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 852 " --> pdb=" O HIS A 840 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 858 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 834 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 819 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 776 through 782 removed outlier: 5.591A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.402A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR A 941 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU A 900 " --> pdb=" O THR A 941 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB9, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AC1, first strand: chain 'B' and resid 62 through 63 removed outlier: 3.512A pdb=" N MET B 187 " --> pdb=" O HIS B 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 149 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.661A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.901A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 230 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.901A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 230 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 265 through 273 removed outlier: 5.695A pdb=" N GLN B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN B 262 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 311 " --> pdb=" O CYS B 328 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC7, first strand: chain 'B' and resid 351 through 354 removed outlier: 7.262A pdb=" N LEU B 533 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY B 565 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 535 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 567 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLU B 537 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 386 through 387 removed outlier: 6.893A pdb=" N VAL B 387 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLU B 412 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 411 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 575 through 578 removed outlier: 3.684A pdb=" N LEU B 575 " --> pdb=" O ALA B 587 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AD2, first strand: chain 'B' and resid 661 through 669 removed outlier: 6.529A pdb=" N VAL B 656 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER B 665 " --> pdb=" O TRP B 654 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP B 654 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU B 667 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 652 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY B 692 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA B 723 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 694 " --> pdb=" O ARG B 721 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG B 721 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 696 " --> pdb=" O GLN B 719 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN B 719 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 698 " --> pdb=" O TRP B 717 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP B 717 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 700 " --> pdb=" O SER B 715 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 741 through 742 removed outlier: 3.648A pdb=" N GLN B 767 " --> pdb=" O GLN B 757 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 770 " --> pdb=" O LYS B 773 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 773 " --> pdb=" O ILE B 770 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 776 through 782 removed outlier: 5.591A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.402A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.245A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 21.079A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.454A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 852 " --> pdb=" O HIS B 840 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 858 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 834 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 819 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 776 through 782 removed outlier: 5.591A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.402A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR B 941 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU B 900 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD7, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AD8, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.512A pdb=" N MET C 187 " --> pdb=" O HIS C 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C 149 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.661A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.901A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 230 " --> pdb=" O VAL C 239 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.901A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 230 " --> pdb=" O VAL C 239 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 265 through 273 removed outlier: 5.695A pdb=" N GLN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN C 262 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 311 " --> pdb=" O CYS C 328 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AE5, first strand: chain 'C' and resid 351 through 354 removed outlier: 7.262A pdb=" N LEU C 533 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY C 565 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU C 535 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL C 567 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLU C 537 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 386 through 387 removed outlier: 6.893A pdb=" N VAL C 387 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLU C 412 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP C 411 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 575 through 578 removed outlier: 3.684A pdb=" N LEU C 575 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AE9, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.529A pdb=" N VAL C 656 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER C 665 " --> pdb=" O TRP C 654 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP C 654 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU C 667 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 652 " --> pdb=" O GLU C 667 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY C 692 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA C 723 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 694 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG C 721 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 696 " --> pdb=" O GLN C 719 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN C 719 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 698 " --> pdb=" O TRP C 717 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP C 717 " --> pdb=" O VAL C 698 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 700 " --> pdb=" O SER C 715 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 741 through 742 removed outlier: 3.648A pdb=" N GLN C 767 " --> pdb=" O GLN C 757 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 770 " --> pdb=" O LYS C 773 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS C 773 " --> pdb=" O ILE C 770 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 776 through 782 removed outlier: 5.591A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.402A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.245A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 21.079A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.454A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 852 " --> pdb=" O HIS C 840 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 858 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 834 " --> pdb=" O ILE C 858 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 819 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 776 through 782 removed outlier: 5.591A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.402A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR C 941 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU C 900 " --> pdb=" O THR C 941 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AF5, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AF6, first strand: chain 'D' and resid 62 through 63 removed outlier: 3.512A pdb=" N MET D 187 " --> pdb=" O HIS D 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 149 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.661A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.901A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 230 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.901A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 230 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 265 through 273 removed outlier: 5.695A pdb=" N GLN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN D 262 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 311 " --> pdb=" O CYS D 328 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AG3, first strand: chain 'D' and resid 351 through 354 removed outlier: 7.262A pdb=" N LEU D 533 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY D 565 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU D 535 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL D 567 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLU D 537 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 386 through 387 removed outlier: 6.893A pdb=" N VAL D 387 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLU D 412 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP D 411 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'D' and resid 575 through 578 removed outlier: 3.684A pdb=" N LEU D 575 " --> pdb=" O ALA D 587 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AG7, first strand: chain 'D' and resid 661 through 669 removed outlier: 6.529A pdb=" N VAL D 656 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER D 665 " --> pdb=" O TRP D 654 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP D 654 " --> pdb=" O SER D 665 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU D 667 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU D 652 " --> pdb=" O GLU D 667 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY D 692 " --> pdb=" O ALA D 723 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA D 723 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU D 694 " --> pdb=" O ARG D 721 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG D 721 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU D 696 " --> pdb=" O GLN D 719 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN D 719 " --> pdb=" O LEU D 696 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL D 698 " --> pdb=" O TRP D 717 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP D 717 " --> pdb=" O VAL D 698 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL D 700 " --> pdb=" O SER D 715 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 741 through 742 removed outlier: 3.648A pdb=" N GLN D 767 " --> pdb=" O GLN D 757 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 770 " --> pdb=" O LYS D 773 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS D 773 " --> pdb=" O ILE D 770 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 776 through 782 removed outlier: 5.591A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.402A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.245A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 21.079A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.454A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 852 " --> pdb=" O HIS D 840 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 858 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 834 " --> pdb=" O ILE D 858 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU D 819 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 776 through 782 removed outlier: 5.591A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.402A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR D 941 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU D 900 " --> pdb=" O THR D 941 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3024 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: 9.22 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8880 1.33 - 1.45: 6544 1.45 - 1.58: 17324 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 32988 Sorted by residual: bond pdb=" N CYS A 825 " pdb=" CA CYS A 825 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.94e+00 bond pdb=" N CYS B 825 " pdb=" CA CYS B 825 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.94e+00 bond pdb=" N CYS C 825 " pdb=" CA CYS C 825 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.94e+00 bond pdb=" N CYS D 825 " pdb=" CA CYS D 825 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.94e+00 bond pdb=" N VAL C 795 " pdb=" CA VAL C 795 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.72e+00 ... (remaining 32983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 43608 1.93 - 3.85: 1256 3.85 - 5.78: 116 5.78 - 7.70: 12 7.70 - 9.63: 12 Bond angle restraints: 45004 Sorted by residual: angle pdb=" N PHE A 176 " pdb=" CA PHE A 176 " pdb=" C PHE A 176 " ideal model delta sigma weight residual 113.89 107.58 6.31 1.58e+00 4.01e-01 1.60e+01 angle pdb=" N PHE D 176 " pdb=" CA PHE D 176 " pdb=" C PHE D 176 " ideal model delta sigma weight residual 113.89 107.58 6.31 1.58e+00 4.01e-01 1.60e+01 angle pdb=" N PHE B 176 " pdb=" CA PHE B 176 " pdb=" C PHE B 176 " ideal model delta sigma weight residual 113.89 107.58 6.31 1.58e+00 4.01e-01 1.60e+01 angle pdb=" N PHE C 176 " pdb=" CA PHE C 176 " pdb=" C PHE C 176 " ideal model delta sigma weight residual 113.89 107.58 6.31 1.58e+00 4.01e-01 1.60e+01 angle pdb=" CA GLY A 459 " pdb=" C GLY A 459 " pdb=" O GLY A 459 " ideal model delta sigma weight residual 122.05 118.33 3.72 1.00e+00 1.00e+00 1.38e+01 ... (remaining 44999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 17124 17.37 - 34.75: 1604 34.75 - 52.12: 396 52.12 - 69.49: 104 69.49 - 86.87: 68 Dihedral angle restraints: 19296 sinusoidal: 7784 harmonic: 11512 Sorted by residual: dihedral pdb=" CA TRP D 518 " pdb=" C TRP D 518 " pdb=" N SER D 519 " pdb=" CA SER D 519 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TRP C 518 " pdb=" C TRP C 518 " pdb=" N SER C 519 " pdb=" CA SER C 519 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TRP B 518 " pdb=" C TRP B 518 " pdb=" N SER B 519 " pdb=" CA SER B 519 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 19293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4056 0.070 - 0.139: 572 0.139 - 0.209: 68 0.209 - 0.279: 4 0.279 - 0.348: 4 Chirality restraints: 4704 Sorted by residual: chirality pdb=" CG LEU C 822 " pdb=" CB LEU C 822 " pdb=" CD1 LEU C 822 " pdb=" CD2 LEU C 822 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CG LEU D 822 " pdb=" CB LEU D 822 " pdb=" CD1 LEU D 822 " pdb=" CD2 LEU D 822 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CG LEU A 822 " pdb=" CB LEU A 822 " pdb=" CD1 LEU A 822 " pdb=" CD2 LEU A 822 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 4701 not shown) Planarity restraints: 5928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 544 " 0.029 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C ASN C 544 " -0.097 2.00e-02 2.50e+03 pdb=" O ASN C 544 " 0.036 2.00e-02 2.50e+03 pdb=" N SER C 545 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 544 " 0.029 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C ASN B 544 " -0.097 2.00e-02 2.50e+03 pdb=" O ASN B 544 " 0.036 2.00e-02 2.50e+03 pdb=" N SER B 545 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 544 " -0.029 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C ASN A 544 " 0.097 2.00e-02 2.50e+03 pdb=" O ASN A 544 " -0.036 2.00e-02 2.50e+03 pdb=" N SER A 545 " -0.032 2.00e-02 2.50e+03 ... (remaining 5925 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.92: 40 1.92 - 2.66: 884 2.66 - 3.41: 44888 3.41 - 4.15: 83666 4.15 - 4.90: 147498 Nonbonded interactions: 276976 Sorted by model distance: nonbonded pdb=" OE2 GLU D 487 " pdb=" SG CYS D 536 " model vdw 1.172 3.400 nonbonded pdb=" OE2 GLU C 487 " pdb=" SG CYS C 536 " model vdw 1.172 3.400 nonbonded pdb=" OE2 GLU A 487 " pdb=" SG CYS A 536 " model vdw 1.172 3.400 nonbonded pdb=" OE2 GLU B 487 " pdb=" SG CYS B 536 " model vdw 1.172 3.400 nonbonded pdb=" NE ARG C 599 " pdb=" OE2 GLU C 797 " model vdw 1.489 3.120 ... (remaining 276971 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 37.250 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 : 0.004 0.079 32996 Z= 0.275 Angle : 0.692 9.627 45004 Z= 0.413 Chirality : 0.050 0.348 4704 Planarity : 0.005 0.076 5928 Dihedral : 15.759 86.865 11872 Min Nonbonded Distance : 1.172 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.67 % Favored : 95.03 % Rotamer: Outliers : 0.23 % Allowed : 16.51 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3944 helix: -0.49 (0.22), residues: 564 sheet: 0.02 (0.15), residues: 1256 loop : -0.75 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1013 TYR 0.014 0.001 TYR D 392 PHE 0.011 0.001 PHE D 989 TRP 0.044 0.002 TRP D 73 HIS 0.004 0.001 HIS C 464 Details of bonding type rmsd covalent geometry : bond 0.00392 (32988) covalent geometry : angle 0.69211 (45004) hydrogen bonds : bond 0.22266 ( 1076) hydrogen bonds : angle 9.21643 ( 3024) Misc. bond : bond 0.06067 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 234 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 MET cc_start: 0.8614 (ptm) cc_final: 0.8295 (ppp) REVERT: A 968 MET cc_start: 0.4965 (mtt) cc_final: 0.4489 (mtt) REVERT: B 655 MET cc_start: 0.8653 (ptm) cc_final: 0.8353 (ppp) REVERT: B 968 MET cc_start: 0.4973 (mtt) cc_final: 0.4517 (mtt) REVERT: C 655 MET cc_start: 0.8654 (ptm) cc_final: 0.8352 (ppp) REVERT: C 968 MET cc_start: 0.4980 (mtt) cc_final: 0.3561 (ptp) REVERT: D 655 MET cc_start: 0.8663 (ptm) cc_final: 0.8352 (ppp) REVERT: D 968 MET cc_start: 0.4543 (mtt) cc_final: 0.3164 (ptp) outliers start: 8 outliers final: 4 residues processed: 242 average time/residue: 0.2183 time to fit residues: 85.5831 Evaluate side-chains 146 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain D residue 549 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 GLN A 890 GLN B 50 GLN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN B 624 GLN C 50 GLN ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN C 624 GLN C 890 GLN D 50 GLN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN D 624 GLN D 887 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.105041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065313 restraints weight = 112087.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.067912 restraints weight = 60191.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.069342 restraints weight = 44464.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.070218 restraints weight = 38334.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.070600 restraints weight = 35526.272| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 32996 Z= 0.335 Angle : 0.762 9.908 45004 Z= 0.393 Chirality : 0.047 0.152 4704 Planarity : 0.006 0.046 5928 Dihedral : 5.346 44.499 4352 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.54 % Allowed : 14.20 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 3944 helix: -0.57 (0.21), residues: 564 sheet: -0.29 (0.14), residues: 1204 loop : -0.95 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 388 TYR 0.021 0.003 TYR B 285 PHE 0.021 0.002 PHE B 143 TRP 0.020 0.002 TRP D 73 HIS 0.027 0.002 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00737 (32988) covalent geometry : angle 0.76183 (45004) hydrogen bonds : bond 0.05138 ( 1076) hydrogen bonds : angle 6.80864 ( 3024) Misc. bond : bond 0.00286 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 148 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 144 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7627 (t0) REVERT: A 202 MET cc_start: 0.8715 (ptm) cc_final: 0.8237 (ppp) REVERT: A 246 MET cc_start: 0.8642 (ptp) cc_final: 0.8292 (pmm) REVERT: A 412 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: A 603 MET cc_start: 0.7580 (tpp) cc_final: 0.6947 (tpp) REVERT: A 606 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8829 (mp) REVERT: A 655 MET cc_start: 0.9271 (ptm) cc_final: 0.8512 (ppp) REVERT: A 768 MET cc_start: 0.8708 (tmm) cc_final: 0.8504 (tmm) REVERT: A 888 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.8748 (tp) REVERT: A 968 MET cc_start: 0.5537 (mtt) cc_final: 0.5197 (mtt) REVERT: B 99 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 144 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7592 (t0) REVERT: B 202 MET cc_start: 0.8720 (ptm) cc_final: 0.8244 (ppp) REVERT: B 246 MET cc_start: 0.8651 (ptp) cc_final: 0.8308 (pmm) REVERT: B 412 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: B 603 MET cc_start: 0.7585 (tpp) cc_final: 0.6948 (tpp) REVERT: B 655 MET cc_start: 0.9274 (ptm) cc_final: 0.8668 (ppp) REVERT: B 888 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.8740 (tp) REVERT: B 968 MET cc_start: 0.5527 (mtt) cc_final: 0.5186 (mtt) REVERT: C 99 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8378 (mp) REVERT: C 144 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7594 (t0) REVERT: C 202 MET cc_start: 0.8719 (ptm) cc_final: 0.8245 (ppp) REVERT: C 246 MET cc_start: 0.8654 (ptp) cc_final: 0.8303 (pmm) REVERT: C 412 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: C 603 MET cc_start: 0.7580 (tpp) cc_final: 0.6941 (tpp) REVERT: C 655 MET cc_start: 0.9273 (ptm) cc_final: 0.8512 (ppp) REVERT: C 888 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8734 (tp) REVERT: C 968 MET cc_start: 0.5549 (mtt) cc_final: 0.5204 (mtt) REVERT: D 99 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8441 (mp) REVERT: D 144 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7620 (t0) REVERT: D 202 MET cc_start: 0.8719 (ptm) cc_final: 0.8254 (ppp) REVERT: D 246 MET cc_start: 0.8630 (ptp) cc_final: 0.8293 (pmm) REVERT: D 412 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: D 603 MET cc_start: 0.7567 (tpp) cc_final: 0.6939 (tpp) REVERT: D 655 MET cc_start: 0.9275 (ptm) cc_final: 0.8516 (ppp) REVERT: D 768 MET cc_start: 0.8695 (tmm) cc_final: 0.8495 (tmm) REVERT: D 888 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.8737 (tp) REVERT: D 968 MET cc_start: 0.5546 (mtt) cc_final: 0.5198 (mtt) outliers start: 155 outliers final: 65 residues processed: 293 average time/residue: 0.1579 time to fit residues: 80.9087 Evaluate side-chains 217 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 135 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 523 TRP Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 856 TYR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 523 TRP Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 856 TYR Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 412 GLU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 523 TRP Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 696 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 856 TYR Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 927 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 108 optimal weight: 0.9980 chunk 297 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 246 optimal weight: 0.4980 chunk 115 optimal weight: 0.7980 chunk 237 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 284 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 GLN A 675 GLN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 GLN B 675 GLN B 887 GLN B 890 GLN ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 GLN C 675 GLN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 GLN D 675 GLN D 890 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.107338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068635 restraints weight = 110867.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.071510 restraints weight = 56925.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.073218 restraints weight = 41181.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.074113 restraints weight = 35023.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.074594 restraints weight = 32348.256| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32996 Z= 0.121 Angle : 0.614 14.364 45004 Z= 0.308 Chirality : 0.044 0.143 4704 Planarity : 0.004 0.033 5928 Dihedral : 4.915 42.666 4352 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.84 % Allowed : 15.93 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 3944 helix: -0.03 (0.22), residues: 568 sheet: -0.06 (0.14), residues: 1208 loop : -0.81 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 388 TYR 0.012 0.001 TYR D1016 PHE 0.010 0.001 PHE D 989 TRP 0.015 0.001 TRP B 518 HIS 0.011 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00266 (32988) covalent geometry : angle 0.61424 (45004) hydrogen bonds : bond 0.03934 ( 1076) hydrogen bonds : angle 5.86644 ( 3024) Misc. bond : bond 0.00163 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 153 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 144 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8053 (t0) REVERT: A 202 MET cc_start: 0.8606 (ptm) cc_final: 0.8249 (ppp) REVERT: A 246 MET cc_start: 0.8574 (ptp) cc_final: 0.8246 (pmm) REVERT: A 367 MET cc_start: 0.7477 (mmm) cc_final: 0.6976 (mmm) REVERT: A 606 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8859 (mp) REVERT: A 655 MET cc_start: 0.9248 (ptm) cc_final: 0.8494 (ppp) REVERT: A 888 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8786 (tp) REVERT: A 968 MET cc_start: 0.5579 (mtt) cc_final: 0.5234 (mtt) REVERT: B 99 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8687 (mp) REVERT: B 144 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8044 (t0) REVERT: B 202 MET cc_start: 0.8598 (ptm) cc_final: 0.8253 (ppp) REVERT: B 246 MET cc_start: 0.8597 (ptp) cc_final: 0.8263 (pmm) REVERT: B 367 MET cc_start: 0.7508 (mmm) cc_final: 0.7005 (mmm) REVERT: B 606 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8779 (mp) REVERT: B 655 MET cc_start: 0.9249 (ptm) cc_final: 0.8499 (ppp) REVERT: B 888 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8785 (tp) REVERT: B 968 MET cc_start: 0.5577 (mtt) cc_final: 0.5230 (mtt) REVERT: C 99 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8641 (mp) REVERT: C 144 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8053 (t0) REVERT: C 202 MET cc_start: 0.8617 (ptm) cc_final: 0.8262 (ppp) REVERT: C 246 MET cc_start: 0.8597 (ptp) cc_final: 0.8256 (pmm) REVERT: C 254 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7566 (pp) REVERT: C 367 MET cc_start: 0.7506 (mmm) cc_final: 0.7008 (mmm) REVERT: C 606 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8775 (mp) REVERT: C 655 MET cc_start: 0.9249 (ptm) cc_final: 0.8495 (ppp) REVERT: C 888 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8754 (tp) REVERT: C 968 MET cc_start: 0.5599 (mtt) cc_final: 0.5251 (mtt) REVERT: D 99 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8635 (mp) REVERT: D 144 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8132 (t0) REVERT: D 202 MET cc_start: 0.8610 (ptm) cc_final: 0.8259 (ppp) REVERT: D 246 MET cc_start: 0.8590 (ptp) cc_final: 0.8258 (pmm) REVERT: D 254 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7577 (pp) REVERT: D 367 MET cc_start: 0.7481 (mmm) cc_final: 0.6986 (mmm) REVERT: D 606 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8850 (mp) REVERT: D 655 MET cc_start: 0.9252 (ptm) cc_final: 0.8498 (ppp) REVERT: D 888 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8789 (tp) REVERT: D 968 MET cc_start: 0.5584 (mtt) cc_final: 0.5235 (mtt) outliers start: 97 outliers final: 44 residues processed: 242 average time/residue: 0.1779 time to fit residues: 75.4167 Evaluate side-chains 202 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 140 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 856 TYR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 856 TYR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 856 TYR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 927 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 178 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 325 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 360 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 50 GLN ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.105498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.066356 restraints weight = 111370.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.069028 restraints weight = 58859.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.070638 restraints weight = 43227.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.071480 restraints weight = 37053.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.071852 restraints weight = 34366.434| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 32996 Z= 0.207 Angle : 0.619 10.464 45004 Z= 0.312 Chirality : 0.043 0.143 4704 Planarity : 0.004 0.033 5928 Dihedral : 4.926 40.751 4352 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.78 % Allowed : 15.69 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 3944 helix: 0.05 (0.22), residues: 568 sheet: -0.01 (0.15), residues: 1128 loop : -0.95 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 388 TYR 0.015 0.002 TYR C 285 PHE 0.028 0.001 PHE D 989 TRP 0.016 0.001 TRP A 523 HIS 0.009 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00458 (32988) covalent geometry : angle 0.61881 (45004) hydrogen bonds : bond 0.03679 ( 1076) hydrogen bonds : angle 5.69706 ( 3024) Misc. bond : bond 0.00090 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 139 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8742 (mp) REVERT: A 144 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7904 (t0) REVERT: A 187 MET cc_start: 0.8022 (ppp) cc_final: 0.7573 (ppp) REVERT: A 202 MET cc_start: 0.8681 (ptm) cc_final: 0.8403 (ppp) REVERT: A 246 MET cc_start: 0.8528 (ptp) cc_final: 0.8262 (pmm) REVERT: A 379 MET cc_start: 0.9056 (ttm) cc_final: 0.8738 (mtm) REVERT: A 542 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6555 (mmm) REVERT: A 606 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8766 (mp) REVERT: A 655 MET cc_start: 0.9259 (ptm) cc_final: 0.8492 (ppp) REVERT: A 968 MET cc_start: 0.5655 (mtt) cc_final: 0.5296 (mtt) REVERT: B 99 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8733 (mp) REVERT: B 144 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7903 (t0) REVERT: B 187 MET cc_start: 0.8027 (ppp) cc_final: 0.7575 (ppp) REVERT: B 202 MET cc_start: 0.8686 (ptm) cc_final: 0.8415 (ppp) REVERT: B 246 MET cc_start: 0.8556 (ptp) cc_final: 0.8281 (pmm) REVERT: B 379 MET cc_start: 0.9068 (ttm) cc_final: 0.8704 (mtm) REVERT: B 542 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6573 (mmm) REVERT: B 606 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8720 (mp) REVERT: B 655 MET cc_start: 0.9257 (ptm) cc_final: 0.8498 (ppp) REVERT: B 968 MET cc_start: 0.5660 (mtt) cc_final: 0.5302 (mtt) REVERT: C 99 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8736 (mp) REVERT: C 144 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7930 (t0) REVERT: C 187 MET cc_start: 0.8017 (ppp) cc_final: 0.7569 (ppp) REVERT: C 202 MET cc_start: 0.8602 (ptm) cc_final: 0.8306 (ppp) REVERT: C 246 MET cc_start: 0.8670 (ptp) cc_final: 0.8283 (pmm) REVERT: C 542 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6554 (mmm) REVERT: C 606 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8714 (mp) REVERT: C 655 MET cc_start: 0.9258 (ptm) cc_final: 0.8492 (ppp) REVERT: C 968 MET cc_start: 0.5682 (mtt) cc_final: 0.5321 (mtt) REVERT: D 99 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8730 (mp) REVERT: D 144 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7915 (t0) REVERT: D 187 MET cc_start: 0.8007 (ppp) cc_final: 0.7561 (ppp) REVERT: D 202 MET cc_start: 0.8674 (ptm) cc_final: 0.8406 (ppp) REVERT: D 246 MET cc_start: 0.8639 (ptp) cc_final: 0.8278 (pmm) REVERT: D 379 MET cc_start: 0.9051 (ttm) cc_final: 0.8728 (mtm) REVERT: D 542 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6537 (mmm) REVERT: D 606 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8718 (mp) REVERT: D 655 MET cc_start: 0.9261 (ptm) cc_final: 0.8497 (ppp) REVERT: D 968 MET cc_start: 0.5672 (mtt) cc_final: 0.5308 (mtt) outliers start: 95 outliers final: 68 residues processed: 230 average time/residue: 0.1525 time to fit residues: 62.3093 Evaluate side-chains 214 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 130 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 523 TRP Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 856 TYR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 523 TRP Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 856 TYR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 357 HIS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 523 TRP Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 696 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 856 TYR Chi-restraints excluded: chain D residue 927 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 266 optimal weight: 20.0000 chunk 385 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 379 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 84 optimal weight: 30.0000 chunk 365 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 335 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 chunk 361 optimal weight: 20.0000 overall best weight: 6.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 ASN ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.102281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.062393 restraints weight = 114211.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065157 restraints weight = 72655.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065468 restraints weight = 48893.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065751 restraints weight = 49918.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.065971 restraints weight = 46857.400| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 32996 Z= 0.455 Angle : 0.828 12.211 45004 Z= 0.427 Chirality : 0.050 0.204 4704 Planarity : 0.006 0.059 5928 Dihedral : 5.601 37.792 4352 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.72 % Allowed : 17.30 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 3944 helix: -0.78 (0.21), residues: 540 sheet: -0.57 (0.14), residues: 1244 loop : -1.03 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 388 TYR 0.019 0.003 TYR C 588 PHE 0.021 0.003 PHE A 989 TRP 0.019 0.002 TRP C 553 HIS 0.013 0.003 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00991 (32988) covalent geometry : angle 0.82803 (45004) hydrogen bonds : bond 0.04647 ( 1076) hydrogen bonds : angle 6.37602 ( 3024) Misc. bond : bond 0.00132 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 128 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8958 (tp) REVERT: A 144 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7632 (t0) REVERT: A 187 MET cc_start: 0.8263 (ppp) cc_final: 0.8060 (ppp) REVERT: A 202 MET cc_start: 0.8480 (ptm) cc_final: 0.8235 (ppp) REVERT: A 246 MET cc_start: 0.8759 (ptp) cc_final: 0.8392 (pmm) REVERT: A 375 ASP cc_start: 0.9527 (OUTLIER) cc_final: 0.9081 (t70) REVERT: A 379 MET cc_start: 0.9175 (ttm) cc_final: 0.8814 (mtm) REVERT: A 603 MET cc_start: 0.8038 (tpp) cc_final: 0.7546 (tpt) REVERT: A 606 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9002 (mp) REVERT: A 655 MET cc_start: 0.9271 (ptm) cc_final: 0.8672 (ppp) REVERT: A 968 MET cc_start: 0.5787 (mtt) cc_final: 0.5380 (mtt) REVERT: B 99 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8959 (tp) REVERT: B 144 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7633 (t0) REVERT: B 187 MET cc_start: 0.8260 (ppp) cc_final: 0.8059 (ppp) REVERT: B 202 MET cc_start: 0.8465 (ptm) cc_final: 0.8236 (ppp) REVERT: B 246 MET cc_start: 0.8762 (ptp) cc_final: 0.8400 (pmm) REVERT: B 375 ASP cc_start: 0.9528 (OUTLIER) cc_final: 0.9079 (t70) REVERT: B 379 MET cc_start: 0.9180 (ttm) cc_final: 0.8782 (mtm) REVERT: B 603 MET cc_start: 0.8060 (tpp) cc_final: 0.7578 (tpt) REVERT: B 606 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9002 (mp) REVERT: B 655 MET cc_start: 0.9272 (ptm) cc_final: 0.8682 (ppp) REVERT: B 968 MET cc_start: 0.5797 (mtt) cc_final: 0.5387 (mtt) REVERT: C 99 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8965 (tp) REVERT: C 144 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7623 (t0) REVERT: C 202 MET cc_start: 0.8469 (ptm) cc_final: 0.8200 (ppp) REVERT: C 246 MET cc_start: 0.8819 (ptp) cc_final: 0.8392 (pmm) REVERT: C 375 ASP cc_start: 0.9493 (OUTLIER) cc_final: 0.9078 (t70) REVERT: C 603 MET cc_start: 0.8067 (tpp) cc_final: 0.7596 (tpt) REVERT: C 606 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9000 (mp) REVERT: C 655 MET cc_start: 0.9273 (ptm) cc_final: 0.8674 (ppp) REVERT: C 968 MET cc_start: 0.5805 (mtt) cc_final: 0.5393 (mtt) REVERT: D 99 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8965 (tp) REVERT: D 144 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7631 (t0) REVERT: D 187 MET cc_start: 0.8262 (ppp) cc_final: 0.8052 (ppp) REVERT: D 202 MET cc_start: 0.8442 (ptm) cc_final: 0.8231 (ppp) REVERT: D 246 MET cc_start: 0.8823 (ptp) cc_final: 0.8398 (pmm) REVERT: D 375 ASP cc_start: 0.9545 (OUTLIER) cc_final: 0.9090 (t70) REVERT: D 379 MET cc_start: 0.9173 (ttm) cc_final: 0.8794 (mtm) REVERT: D 603 MET cc_start: 0.8021 (tpp) cc_final: 0.7520 (tpt) REVERT: D 606 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9005 (mp) REVERT: D 655 MET cc_start: 0.9274 (ptm) cc_final: 0.8677 (ppp) REVERT: D 968 MET cc_start: 0.5803 (mtt) cc_final: 0.5393 (mtt) outliers start: 127 outliers final: 84 residues processed: 251 average time/residue: 0.1575 time to fit residues: 70.1432 Evaluate side-chains 224 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 124 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 523 TRP Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 856 TYR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 523 TRP Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 601 PHE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 856 TYR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 523 TRP Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 696 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 856 TYR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 927 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 69 optimal weight: 5.9990 chunk 240 optimal weight: 0.7980 chunk 85 optimal weight: 0.0370 chunk 114 optimal weight: 1.9990 chunk 394 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 392 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN D 50 GLN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN ** D 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.104954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.065972 restraints weight = 111991.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.068663 restraints weight = 59173.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.070213 restraints weight = 43442.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.071034 restraints weight = 37473.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.071483 restraints weight = 34783.015| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32996 Z= 0.144 Angle : 0.595 7.476 45004 Z= 0.301 Chirality : 0.043 0.141 4704 Planarity : 0.004 0.036 5928 Dihedral : 4.989 39.261 4352 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.37 % Allowed : 18.21 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 3944 helix: -0.22 (0.22), residues: 564 sheet: -0.02 (0.15), residues: 1116 loop : -0.99 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 442 TYR 0.012 0.001 TYR B 588 PHE 0.017 0.001 PHE A 989 TRP 0.016 0.001 TRP B 518 HIS 0.008 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00317 (32988) covalent geometry : angle 0.59517 (45004) hydrogen bonds : bond 0.03529 ( 1076) hydrogen bonds : angle 5.54954 ( 3024) Misc. bond : bond 0.00111 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 139 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7802 (t0) REVERT: A 187 MET cc_start: 0.8123 (ppp) cc_final: 0.7916 (ppp) REVERT: A 606 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 655 MET cc_start: 0.9256 (ptm) cc_final: 0.8667 (ppp) REVERT: A 968 MET cc_start: 0.5788 (mtt) cc_final: 0.5372 (mtt) REVERT: A 991 MET cc_start: 0.7799 (tpt) cc_final: 0.7508 (tpp) REVERT: B 144 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7795 (t0) REVERT: B 187 MET cc_start: 0.8126 (ppp) cc_final: 0.7918 (ppp) REVERT: B 349 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8707 (tp) REVERT: B 606 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8706 (mp) REVERT: B 655 MET cc_start: 0.9257 (ptm) cc_final: 0.8672 (ppp) REVERT: B 968 MET cc_start: 0.5794 (mtt) cc_final: 0.5375 (mtt) REVERT: B 991 MET cc_start: 0.7798 (tpt) cc_final: 0.7507 (tpp) REVERT: C 144 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7792 (t0) REVERT: C 202 MET cc_start: 0.8554 (ptm) cc_final: 0.8315 (ppp) REVERT: C 606 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8715 (mp) REVERT: C 655 MET cc_start: 0.9257 (ptm) cc_final: 0.8670 (ppp) REVERT: C 968 MET cc_start: 0.5805 (mtt) cc_final: 0.5386 (mtt) REVERT: C 991 MET cc_start: 0.7798 (tpt) cc_final: 0.7509 (tpp) REVERT: D 144 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7643 (t0) REVERT: D 187 MET cc_start: 0.8122 (ppp) cc_final: 0.7913 (ppp) REVERT: D 606 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8701 (mp) REVERT: D 655 MET cc_start: 0.9259 (ptm) cc_final: 0.8671 (ppp) REVERT: D 925 MET cc_start: 0.7330 (mmm) cc_final: 0.6588 (mmm) REVERT: D 968 MET cc_start: 0.5804 (mtt) cc_final: 0.5384 (mtt) REVERT: D 991 MET cc_start: 0.7801 (tpt) cc_final: 0.7511 (tpp) outliers start: 81 outliers final: 63 residues processed: 213 average time/residue: 0.1637 time to fit residues: 61.3489 Evaluate side-chains 204 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 132 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 523 TRP Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 856 TYR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 523 TRP Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 856 TYR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 357 HIS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 523 TRP Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 856 TYR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 927 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 308 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 335 optimal weight: 1.9990 chunk 345 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 389 optimal weight: 0.6980 chunk 363 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN ** D 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.104161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065001 restraints weight = 112949.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.067424 restraints weight = 63334.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.068857 restraints weight = 47731.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.069553 restraints weight = 41478.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.070011 restraints weight = 38700.712| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32996 Z= 0.210 Angle : 0.620 8.715 45004 Z= 0.313 Chirality : 0.043 0.146 4704 Planarity : 0.004 0.034 5928 Dihedral : 4.982 38.635 4352 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.43 % Allowed : 18.33 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 3944 helix: -0.18 (0.22), residues: 564 sheet: -0.10 (0.15), residues: 1088 loop : -1.05 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 388 TYR 0.012 0.001 TYR B 588 PHE 0.016 0.001 PHE A 143 TRP 0.015 0.002 TRP A 523 HIS 0.008 0.001 HIS D 391 Details of bonding type rmsd covalent geometry : bond 0.00465 (32988) covalent geometry : angle 0.62009 (45004) hydrogen bonds : bond 0.03527 ( 1076) hydrogen bonds : angle 5.54588 ( 3024) Misc. bond : bond 0.00071 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 133 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7696 (t0) REVERT: A 187 MET cc_start: 0.8220 (ppp) cc_final: 0.7969 (ppp) REVERT: A 247 CYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8526 (t) REVERT: A 606 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 655 MET cc_start: 0.9259 (ptm) cc_final: 0.8664 (ppp) REVERT: A 968 MET cc_start: 0.5827 (mtt) cc_final: 0.5409 (mtt) REVERT: A 991 MET cc_start: 0.7750 (tpt) cc_final: 0.7530 (tpp) REVERT: B 144 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7692 (t0) REVERT: B 187 MET cc_start: 0.8224 (ppp) cc_final: 0.7970 (ppp) REVERT: B 247 CYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8527 (t) REVERT: B 606 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8760 (mp) REVERT: B 655 MET cc_start: 0.9257 (ptm) cc_final: 0.8667 (ppp) REVERT: B 768 MET cc_start: 0.8938 (tmm) cc_final: 0.8724 (tmm) REVERT: B 968 MET cc_start: 0.5835 (mtt) cc_final: 0.5420 (mtt) REVERT: B 991 MET cc_start: 0.7756 (tpt) cc_final: 0.7534 (tpp) REVERT: C 92 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7837 (ttm) REVERT: C 144 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7689 (t0) REVERT: C 247 CYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8417 (t) REVERT: C 606 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8761 (mp) REVERT: C 655 MET cc_start: 0.9261 (ptm) cc_final: 0.8668 (ppp) REVERT: C 768 MET cc_start: 0.8933 (tmm) cc_final: 0.8718 (tmm) REVERT: C 968 MET cc_start: 0.5847 (mtt) cc_final: 0.5430 (mtt) REVERT: C 991 MET cc_start: 0.7751 (tpt) cc_final: 0.7531 (tpp) REVERT: D 144 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7694 (t0) REVERT: D 187 MET cc_start: 0.8220 (ppp) cc_final: 0.7960 (ppp) REVERT: D 247 CYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8412 (t) REVERT: D 606 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8755 (mp) REVERT: D 655 MET cc_start: 0.9264 (ptm) cc_final: 0.8668 (ppp) REVERT: D 968 MET cc_start: 0.5848 (mtt) cc_final: 0.5428 (mtt) REVERT: D 991 MET cc_start: 0.7757 (tpt) cc_final: 0.7446 (tpp) outliers start: 117 outliers final: 79 residues processed: 239 average time/residue: 0.1658 time to fit residues: 69.7811 Evaluate side-chains 222 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 130 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 523 TRP Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 856 TYR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 523 TRP Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 856 TYR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 357 HIS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 523 TRP Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 696 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 856 TYR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 927 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 297 optimal weight: 1.9990 chunk 384 optimal weight: 7.9990 chunk 365 optimal weight: 10.0000 chunk 50 optimal weight: 0.2980 chunk 322 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 179 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 137 optimal weight: 0.4980 chunk 112 optimal weight: 0.0670 chunk 375 optimal weight: 0.5980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 675 GLN A 949 HIS ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 675 GLN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 675 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN D 675 GLN D 949 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.106129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.067486 restraints weight = 112660.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.070324 restraints weight = 58102.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.071982 restraints weight = 42327.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.072849 restraints weight = 36186.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.073211 restraints weight = 33570.800| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32996 Z= 0.105 Angle : 0.595 10.290 45004 Z= 0.295 Chirality : 0.043 0.145 4704 Planarity : 0.004 0.040 5928 Dihedral : 4.715 39.986 4352 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.20 % Allowed : 19.23 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 3944 helix: 0.16 (0.23), residues: 568 sheet: 0.23 (0.15), residues: 1136 loop : -0.90 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 204 TYR 0.011 0.001 TYR D1016 PHE 0.013 0.001 PHE A 989 TRP 0.028 0.001 TRP D 203 HIS 0.006 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00235 (32988) covalent geometry : angle 0.59521 (45004) hydrogen bonds : bond 0.03075 ( 1076) hydrogen bonds : angle 5.08167 ( 3024) Misc. bond : bond 0.00087 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 136 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8233 (ppp) cc_final: 0.7979 (ppp) REVERT: A 606 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8606 (mp) REVERT: A 655 MET cc_start: 0.9249 (ptm) cc_final: 0.8667 (ppp) REVERT: A 925 MET cc_start: 0.7244 (mmm) cc_final: 0.6291 (mmm) REVERT: A 968 MET cc_start: 0.5820 (mtt) cc_final: 0.5412 (mtt) REVERT: B 187 MET cc_start: 0.8234 (ppp) cc_final: 0.7978 (ppp) REVERT: B 606 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8617 (mp) REVERT: B 655 MET cc_start: 0.9248 (ptm) cc_final: 0.8662 (ppp) REVERT: B 925 MET cc_start: 0.7243 (mmm) cc_final: 0.6261 (mmm) REVERT: B 968 MET cc_start: 0.5829 (mtt) cc_final: 0.5456 (mtt) REVERT: C 92 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7633 (ttm) REVERT: C 606 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8603 (mp) REVERT: C 655 MET cc_start: 0.9249 (ptm) cc_final: 0.8661 (ppp) REVERT: C 925 MET cc_start: 0.7244 (mmm) cc_final: 0.6265 (mmm) REVERT: C 968 MET cc_start: 0.5833 (mtt) cc_final: 0.5429 (mtt) REVERT: D 187 MET cc_start: 0.8222 (ppp) cc_final: 0.7965 (ppp) REVERT: D 606 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8607 (mp) REVERT: D 655 MET cc_start: 0.9251 (ptm) cc_final: 0.8660 (ppp) REVERT: D 925 MET cc_start: 0.7219 (mmm) cc_final: 0.6242 (mmm) REVERT: D 968 MET cc_start: 0.5836 (mtt) cc_final: 0.5462 (mtt) outliers start: 75 outliers final: 52 residues processed: 204 average time/residue: 0.1771 time to fit residues: 62.7494 Evaluate side-chains 183 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 523 TRP Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 856 TYR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 523 TRP Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 856 TYR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 523 TRP Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 856 TYR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 927 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 322 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 chunk 392 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 327 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.104858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.065857 restraints weight = 111967.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.068491 restraints weight = 59521.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.070014 restraints weight = 43921.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.070839 restraints weight = 37851.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.071284 restraints weight = 35121.852| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32996 Z= 0.164 Angle : 0.611 15.741 45004 Z= 0.300 Chirality : 0.043 0.164 4704 Planarity : 0.004 0.033 5928 Dihedral : 4.746 39.377 4352 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.08 % Allowed : 19.12 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.13), residues: 3944 helix: 0.03 (0.22), residues: 568 sheet: 0.25 (0.15), residues: 1148 loop : -0.93 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 388 TYR 0.012 0.001 TYR A1016 PHE 0.014 0.001 PHE D 989 TRP 0.016 0.001 TRP C 203 HIS 0.007 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00372 (32988) covalent geometry : angle 0.61132 (45004) hydrogen bonds : bond 0.03206 ( 1076) hydrogen bonds : angle 5.16238 ( 3024) Misc. bond : bond 0.00044 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 130 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 187 MET cc_start: 0.8249 (ppp) cc_final: 0.8013 (ppp) REVERT: A 606 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8681 (mp) REVERT: A 655 MET cc_start: 0.9254 (ptm) cc_final: 0.8491 (ppp) REVERT: A 925 MET cc_start: 0.7385 (mmm) cc_final: 0.6403 (mmm) REVERT: A 968 MET cc_start: 0.5845 (mtt) cc_final: 0.5417 (mtt) REVERT: B 99 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8593 (mp) REVERT: B 187 MET cc_start: 0.8248 (ppp) cc_final: 0.8008 (ppp) REVERT: B 606 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8689 (mp) REVERT: B 655 MET cc_start: 0.9255 (ptm) cc_final: 0.8653 (ppp) REVERT: B 925 MET cc_start: 0.7347 (mmm) cc_final: 0.6490 (mmm) REVERT: B 968 MET cc_start: 0.5859 (mtt) cc_final: 0.5429 (mtt) REVERT: C 92 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7648 (ttm) REVERT: C 606 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8697 (mp) REVERT: C 655 MET cc_start: 0.9254 (ptm) cc_final: 0.8661 (ppp) REVERT: C 925 MET cc_start: 0.7347 (mmm) cc_final: 0.6491 (mmm) REVERT: C 968 MET cc_start: 0.5860 (mtt) cc_final: 0.5431 (mtt) REVERT: D 187 MET cc_start: 0.8242 (ppp) cc_final: 0.8002 (ppp) REVERT: D 606 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8685 (mp) REVERT: D 655 MET cc_start: 0.9256 (ptm) cc_final: 0.8488 (ppp) REVERT: D 925 MET cc_start: 0.7336 (mmm) cc_final: 0.6479 (mmm) REVERT: D 968 MET cc_start: 0.5861 (mtt) cc_final: 0.5431 (mtt) outliers start: 71 outliers final: 56 residues processed: 192 average time/residue: 0.1818 time to fit residues: 61.1637 Evaluate side-chains 193 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 130 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 523 TRP Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 856 TYR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 856 TYR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 357 HIS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 856 TYR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 927 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 386 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 354 optimal weight: 0.0270 chunk 190 optimal weight: 20.0000 chunk 250 optimal weight: 2.9990 chunk 236 optimal weight: 0.5980 chunk 200 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 310 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 HIS ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.104765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065789 restraints weight = 113348.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.068497 restraints weight = 59510.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.070066 restraints weight = 43590.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.070911 restraints weight = 37440.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.071329 restraints weight = 34768.271| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32996 Z= 0.161 Angle : 0.608 11.474 45004 Z= 0.300 Chirality : 0.043 0.144 4704 Planarity : 0.004 0.033 5928 Dihedral : 4.756 39.409 4352 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.11 % Allowed : 19.17 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 3944 helix: -0.14 (0.22), residues: 568 sheet: 0.27 (0.15), residues: 1148 loop : -0.90 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 961 TYR 0.012 0.001 TYR D1016 PHE 0.013 0.001 PHE C 989 TRP 0.026 0.001 TRP C 523 HIS 0.006 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00363 (32988) covalent geometry : angle 0.60758 (45004) hydrogen bonds : bond 0.03215 ( 1076) hydrogen bonds : angle 5.16354 ( 3024) Misc. bond : bond 0.00049 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 137 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 144 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8084 (t0) REVERT: A 170 GLU cc_start: 0.8487 (pm20) cc_final: 0.7852 (pm20) REVERT: A 187 MET cc_start: 0.8246 (ppp) cc_final: 0.7991 (ppp) REVERT: A 606 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8684 (mp) REVERT: A 655 MET cc_start: 0.9260 (ptm) cc_final: 0.8493 (ppp) REVERT: A 925 MET cc_start: 0.7499 (mmm) cc_final: 0.6612 (mmm) REVERT: A 968 MET cc_start: 0.5873 (mtt) cc_final: 0.5442 (mtt) REVERT: B 144 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8080 (t0) REVERT: B 170 GLU cc_start: 0.8491 (pm20) cc_final: 0.7867 (pm20) REVERT: B 187 MET cc_start: 0.8221 (ppp) cc_final: 0.7976 (ppp) REVERT: B 349 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8660 (tp) REVERT: B 606 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8698 (mp) REVERT: B 655 MET cc_start: 0.9262 (ptm) cc_final: 0.8658 (ppp) REVERT: B 925 MET cc_start: 0.7493 (mmm) cc_final: 0.6617 (mmm) REVERT: B 968 MET cc_start: 0.5884 (mtt) cc_final: 0.5450 (mtt) REVERT: C 92 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7665 (ttm) REVERT: C 144 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.8083 (t0) REVERT: C 170 GLU cc_start: 0.8503 (pm20) cc_final: 0.7872 (pm20) REVERT: C 606 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8701 (mp) REVERT: C 655 MET cc_start: 0.9259 (ptm) cc_final: 0.8654 (ppp) REVERT: C 925 MET cc_start: 0.7488 (mmm) cc_final: 0.6615 (mmm) REVERT: C 968 MET cc_start: 0.5888 (mtt) cc_final: 0.5455 (mtt) REVERT: D 144 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8070 (t0) REVERT: D 170 GLU cc_start: 0.8501 (pm20) cc_final: 0.7871 (pm20) REVERT: D 187 MET cc_start: 0.8222 (ppp) cc_final: 0.7974 (ppp) REVERT: D 606 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8689 (mp) REVERT: D 655 MET cc_start: 0.9262 (ptm) cc_final: 0.8489 (ppp) REVERT: D 925 MET cc_start: 0.7479 (mmm) cc_final: 0.6607 (mmm) REVERT: D 968 MET cc_start: 0.5888 (mtt) cc_final: 0.5455 (mtt) outliers start: 72 outliers final: 56 residues processed: 202 average time/residue: 0.1844 time to fit residues: 64.3318 Evaluate side-chains 199 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 132 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 856 TYR Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 856 TYR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 856 TYR Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 357 HIS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 856 TYR Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 927 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 0.0040 chunk 287 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 305 optimal weight: 0.0470 chunk 268 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 381 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 overall best weight: 1.5894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 675 GLN B 365 GLN B 675 GLN B 949 HIS ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 675 GLN ** D 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.105033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066362 restraints weight = 112105.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.069084 restraints weight = 58422.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.070697 restraints weight = 42640.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071527 restraints weight = 36539.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.071994 restraints weight = 33905.819| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32996 Z= 0.135 Angle : 0.587 11.299 45004 Z= 0.289 Chirality : 0.043 0.137 4704 Planarity : 0.004 0.033 5928 Dihedral : 4.670 39.401 4352 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.22 % Allowed : 19.23 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.13), residues: 3944 helix: -0.07 (0.22), residues: 568 sheet: 0.26 (0.15), residues: 1156 loop : -0.84 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 388 TYR 0.012 0.001 TYR D1016 PHE 0.013 0.001 PHE A 989 TRP 0.019 0.001 TRP C 523 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00307 (32988) covalent geometry : angle 0.58725 (45004) hydrogen bonds : bond 0.03062 ( 1076) hydrogen bonds : angle 5.04532 ( 3024) Misc. bond : bond 0.00054 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5694.77 seconds wall clock time: 99 minutes 36.15 seconds (5976.15 seconds total)