Starting phenix.real_space_refine on Thu Nov 20 09:34:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6drv_8908/11_2025/6drv_8908.cif Found real_map, /net/cci-nas-00/data/ceres_data/6drv_8908/11_2025/6drv_8908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6drv_8908/11_2025/6drv_8908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6drv_8908/11_2025/6drv_8908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6drv_8908/11_2025/6drv_8908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6drv_8908/11_2025/6drv_8908.map" } resolution = 2.2 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= 0.006 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 160 5.16 5 C 20796 2.51 5 N 5816 2.21 5 O 6116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32888 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8222 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 958} Chain: "B" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8222 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 958} Chain: "C" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8222 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 958} Chain: "D" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8222 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 958} Time building chain proxies: 8.09, per 1000 atoms: 0.25 Number of scatterers: 32888 At special positions: 0 Unit cell: (191.737, 150.969, 98.735, 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 160 16.00 O 6116 8.00 N 5816 7.00 C 20796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 537 " distance=2.04 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 537 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 537 " distance=2.04 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS D 537 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.6 seconds 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7624 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 52 sheets defined 19.0% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 4.623A pdb=" N ALA A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 19 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 66 through 71 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.890A pdb=" N GLU A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.521A pdb=" N LEU A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.558A pdb=" N THR A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 removed outlier: 4.520A pdb=" N LEU A 427 " --> pdb=" O MET A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 433 through 449 Processing helix chain 'A' and resid 466 through 480 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.087A pdb=" N SER A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.934A pdb=" N TYR A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.700A pdb=" N CYS A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 806 through 815 Processing helix chain 'A' and resid 924 through 927 Processing helix chain 'A' and resid 964 through 971 Processing helix chain 'A' and resid 973 through 977 Processing helix chain 'A' and resid 1005 through 1009 Processing helix chain 'B' and resid 3 through 15 removed outlier: 4.622A pdb=" N ALA B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 19 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 66 through 71 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.890A pdb=" N GLU B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.520A pdb=" N LEU B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 397 through 407 removed outlier: 3.558A pdb=" N THR B 401 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 4.521A pdb=" N LEU B 427 " --> pdb=" O MET B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 433 through 449 Processing helix chain 'B' and resid 466 through 480 Processing helix chain 'B' and resid 520 through 527 removed outlier: 4.087A pdb=" N SER B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.934A pdb=" N TYR B 553 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 604 removed outlier: 3.700A pdb=" N CYS B 603 " --> pdb=" O ARG B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 806 through 815 Processing helix chain 'B' and resid 924 through 927 Processing helix chain 'B' and resid 964 through 971 Processing helix chain 'B' and resid 973 through 977 Processing helix chain 'B' and resid 1005 through 1009 Processing helix chain 'C' and resid 3 through 15 removed outlier: 4.624A pdb=" N ALA C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 15 " --> pdb=" O VAL C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 19 Processing helix chain 'C' and resid 39 through 45 Processing helix chain 'C' and resid 66 through 71 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.889A pdb=" N GLU C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 Processing helix chain 'C' and resid 131 through 137 removed outlier: 3.520A pdb=" N LEU C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 369 through 383 Processing helix chain 'C' and resid 397 through 407 removed outlier: 3.557A pdb=" N THR C 401 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 427 removed outlier: 4.521A pdb=" N LEU C 427 " --> pdb=" O MET C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 432 No H-bonds generated for 'chain 'C' and resid 430 through 432' Processing helix chain 'C' and resid 433 through 449 Processing helix chain 'C' and resid 466 through 480 Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.086A pdb=" N SER C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 removed outlier: 3.935A pdb=" N TYR C 553 " --> pdb=" O GLY C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 604 removed outlier: 3.699A pdb=" N CYS C 603 " --> pdb=" O ARG C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 625 Processing helix chain 'C' and resid 790 through 795 Processing helix chain 'C' and resid 806 through 815 Processing helix chain 'C' and resid 924 through 927 Processing helix chain 'C' and resid 964 through 971 Processing helix chain 'C' and resid 973 through 977 Processing helix chain 'C' and resid 1005 through 1009 Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.624A pdb=" N ALA D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 19 Processing helix chain 'D' and resid 39 through 45 Processing helix chain 'D' and resid 66 through 71 Proline residue: D 71 - end of helix Processing helix chain 'D' and resid 72 through 77 removed outlier: 3.890A pdb=" N GLU D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 Processing helix chain 'D' and resid 131 through 137 removed outlier: 3.520A pdb=" N LEU D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 199 Processing helix chain 'D' and resid 369 through 383 Processing helix chain 'D' and resid 397 through 407 removed outlier: 3.557A pdb=" N THR D 401 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 4.521A pdb=" N LEU D 427 " --> pdb=" O MET D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 433 through 449 Processing helix chain 'D' and resid 466 through 480 Processing helix chain 'D' and resid 520 through 527 removed outlier: 4.087A pdb=" N SER D 526 " --> pdb=" O LYS D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 removed outlier: 3.935A pdb=" N TYR D 553 " --> pdb=" O GLY D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 removed outlier: 3.699A pdb=" N CYS D 603 " --> pdb=" O ARG D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 625 Processing helix chain 'D' and resid 790 through 795 Processing helix chain 'D' and resid 806 through 815 Processing helix chain 'D' and resid 924 through 927 Processing helix chain 'D' and resid 964 through 971 Processing helix chain 'D' and resid 973 through 977 Processing helix chain 'D' and resid 1005 through 1009 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 87 removed outlier: 8.573A pdb=" N GLU A 58 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR A 127 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE A 151 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR A 162 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 153 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 232 removed outlier: 6.622A pdb=" N GLN A 246 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE A 226 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU A 244 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 228 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU A 242 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A 230 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 240 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE A 232 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 238 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 274 removed outlier: 5.634A pdb=" N GLN A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN A 263 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR A 318 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU A 323 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AA7, first strand: chain 'A' and resid 485 through 486 removed outlier: 8.108A pdb=" N GLN A 486 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP A 457 " --> pdb=" O GLN A 486 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 410 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER A 458 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP A 412 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG A 353 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG A 389 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 355 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 534 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE A 567 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 536 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP A 569 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLU A 538 " --> pdb=" O TRP A 569 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 579 Processing sheet with id=AA9, first strand: chain 'A' and resid 628 through 633 Processing sheet with id=AB1, first strand: chain 'A' and resid 662 through 670 removed outlier: 6.182A pdb=" N LEU A 659 " --> pdb=" O PRO A 663 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY A 693 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU A 725 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A 695 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 717 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN A 703 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 715 " --> pdb=" O GLN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 740 through 743 removed outlier: 5.920A pdb=" N ASN A 760 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 766 " --> pdb=" O ASN A 760 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN A 888 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN A 886 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG A 782 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY A 884 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN A 784 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG A 882 " --> pdb=" O GLN A 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 883 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 990 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ASP A 955 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP A 955 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN A1018 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N GLN A 957 " --> pdb=" O HIS A1016 " (cutoff:3.500A) removed outlier: 13.465A pdb=" N HIS A1016 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 20.535A pdb=" N ASN A 959 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 23.695A pdb=" N ARG A1014 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS A 845 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR A 830 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 836 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA A 828 " --> pdb=" O LEU A 836 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 838 " --> pdb=" O CYS A 826 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS A 826 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA A 840 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN A 888 " --> pdb=" O LEU A 778 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN A 886 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG A 782 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY A 884 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN A 784 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG A 882 " --> pdb=" O GLN A 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 883 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 990 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ASP A 955 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP A 952 " --> pdb=" O ASN A 946 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN A 946 " --> pdb=" O TRP A 952 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLY A 954 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU A 944 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 958 " --> pdb=" O CYS A 940 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N CYS A 940 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR A 942 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU A 901 " --> pdb=" O THR A 942 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 87 removed outlier: 8.574A pdb=" N GLU B 58 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR B 127 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE B 151 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR B 162 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 153 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 147 through 148 Processing sheet with id=AB8, first strand: chain 'B' and resid 222 through 232 removed outlier: 6.623A pdb=" N GLN B 246 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 226 " --> pdb=" O GLU B 244 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU B 244 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 228 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU B 242 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 230 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 240 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B 232 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG B 238 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 266 through 274 removed outlier: 5.633A pdb=" N GLN B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN B 263 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR B 318 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU B 323 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AC2, first strand: chain 'B' and resid 485 through 486 removed outlier: 8.108A pdb=" N GLN B 486 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP B 457 " --> pdb=" O GLN B 486 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 410 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER B 458 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP B 412 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG B 353 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG B 389 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 355 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B 534 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE B 567 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 536 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TRP B 569 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLU B 538 " --> pdb=" O TRP B 569 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 576 through 579 Processing sheet with id=AC4, first strand: chain 'B' and resid 628 through 633 Processing sheet with id=AC5, first strand: chain 'B' and resid 662 through 670 removed outlier: 6.182A pdb=" N LEU B 659 " --> pdb=" O PRO B 663 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY B 693 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU B 725 " --> pdb=" O GLY B 693 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 695 " --> pdb=" O LEU B 723 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 717 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN B 703 " --> pdb=" O ILE B 715 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 715 " --> pdb=" O GLN B 703 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 740 through 743 removed outlier: 5.918A pdb=" N ASN B 760 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU B 766 " --> pdb=" O ASN B 760 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN B 888 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN B 886 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG B 782 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 884 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 784 " --> pdb=" O ARG B 882 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG B 882 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 883 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE B 990 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ASP B 955 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP B 955 " --> pdb=" O GLN B1018 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN B1018 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N GLN B 957 " --> pdb=" O HIS B1016 " (cutoff:3.500A) removed outlier: 13.464A pdb=" N HIS B1016 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 20.535A pdb=" N ASN B 959 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 23.696A pdb=" N ARG B1014 " --> pdb=" O ASN B 959 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS B 845 " --> pdb=" O THR B 849 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA B 834 " --> pdb=" O THR B 830 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR B 830 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B 836 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA B 828 " --> pdb=" O LEU B 836 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR B 838 " --> pdb=" O CYS B 826 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS B 826 " --> pdb=" O THR B 838 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA B 840 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN B 888 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN B 886 " --> pdb=" O PRO B 780 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG B 782 " --> pdb=" O GLY B 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 884 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 784 " --> pdb=" O ARG B 882 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG B 882 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 883 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE B 990 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ASP B 955 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP B 952 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN B 946 " --> pdb=" O TRP B 952 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLY B 954 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU B 944 " --> pdb=" O GLY B 954 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE B 958 " --> pdb=" O CYS B 940 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N CYS B 940 " --> pdb=" O PHE B 958 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR B 942 " --> pdb=" O LEU B 901 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 901 " --> pdb=" O THR B 942 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AD1, first strand: chain 'C' and resid 83 through 87 removed outlier: 8.573A pdb=" N GLU C 58 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR C 127 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE C 151 " --> pdb=" O TYR C 162 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR C 162 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU C 153 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AD3, first strand: chain 'C' and resid 222 through 232 removed outlier: 6.623A pdb=" N GLN C 246 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE C 226 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU C 244 " --> pdb=" O PHE C 226 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL C 228 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU C 242 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 230 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 240 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C 232 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG C 238 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 266 through 274 removed outlier: 5.633A pdb=" N GLN C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN C 263 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 318 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU C 323 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 336 through 339 Processing sheet with id=AD6, first strand: chain 'C' and resid 485 through 486 removed outlier: 8.108A pdb=" N GLN C 486 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP C 457 " --> pdb=" O GLN C 486 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 410 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER C 458 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP C 412 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG C 353 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG C 389 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C 355 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C 534 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE C 567 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 536 " --> pdb=" O PHE C 567 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TRP C 569 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLU C 538 " --> pdb=" O TRP C 569 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 576 through 579 Processing sheet with id=AD8, first strand: chain 'C' and resid 628 through 633 Processing sheet with id=AD9, first strand: chain 'C' and resid 662 through 670 removed outlier: 6.182A pdb=" N LEU C 659 " --> pdb=" O PRO C 663 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY C 693 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU C 725 " --> pdb=" O GLY C 693 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU C 695 " --> pdb=" O LEU C 723 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 717 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN C 703 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 715 " --> pdb=" O GLN C 703 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 740 through 743 removed outlier: 5.919A pdb=" N ASN C 760 " --> pdb=" O LEU C 766 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU C 766 " --> pdb=" O ASN C 760 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN C 888 " --> pdb=" O LEU C 778 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN C 886 " --> pdb=" O PRO C 780 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG C 782 " --> pdb=" O GLY C 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 884 " --> pdb=" O ARG C 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN C 784 " --> pdb=" O ARG C 882 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG C 882 " --> pdb=" O GLN C 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 883 " --> pdb=" O GLY C 989 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE C 990 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 12.043A pdb=" N ASP C 955 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP C 955 " --> pdb=" O GLN C1018 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN C1018 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N GLN C 957 " --> pdb=" O HIS C1016 " (cutoff:3.500A) removed outlier: 13.464A pdb=" N HIS C1016 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 20.534A pdb=" N ASN C 959 " --> pdb=" O ARG C1014 " (cutoff:3.500A) removed outlier: 23.696A pdb=" N ARG C1014 " --> pdb=" O ASN C 959 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS C 845 " --> pdb=" O THR C 849 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA C 834 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR C 830 " --> pdb=" O ALA C 834 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 836 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA C 828 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR C 838 " --> pdb=" O CYS C 826 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS C 826 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA C 840 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 777 through 784 removed outlier: 6.324A pdb=" N GLN C 888 " --> pdb=" O LEU C 778 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASN C 886 " --> pdb=" O PRO C 780 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG C 782 " --> pdb=" O GLY C 884 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 884 " --> pdb=" O ARG C 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN C 784 " --> pdb=" O ARG C 882 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG C 882 " --> pdb=" O GLN C 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 883 " --> pdb=" O GLY C 989 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE C 990 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 12.043A pdb=" N ASP C 955 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP C 952 " --> pdb=" O ASN C 946 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN C 946 " --> pdb=" O TRP C 952 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLY C 954 " --> pdb=" O GLU C 944 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU C 944 " --> pdb=" O GLY C 954 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE C 958 " --> pdb=" O CYS C 940 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N CYS C 940 " --> pdb=" O PHE C 958 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR C 942 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU C 901 " --> pdb=" O THR C 942 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AE5, first strand: chain 'D' and resid 83 through 87 removed outlier: 8.573A pdb=" N GLU D 58 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR D 127 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE D 151 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR D 162 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU D 153 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 147 through 148 Processing sheet with id=AE7, first strand: chain 'D' and resid 222 through 232 removed outlier: 6.622A pdb=" N GLN D 246 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE D 226 " --> pdb=" O GLU D 244 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU D 244 " --> pdb=" O PHE D 226 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 228 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU D 242 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR D 230 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 240 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE D 232 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG D 238 " --> pdb=" O PHE D 232 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 266 through 274 removed outlier: 5.633A pdb=" N GLN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN D 263 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR D 318 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU D 323 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 336 through 339 Processing sheet with id=AF1, first strand: chain 'D' and resid 485 through 486 removed outlier: 8.108A pdb=" N GLN D 486 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP D 457 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 410 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER D 458 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP D 412 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ARG D 353 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG D 389 " --> pdb=" O ARG D 353 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL D 355 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU D 534 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE D 567 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU D 536 " --> pdb=" O PHE D 567 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP D 569 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLU D 538 " --> pdb=" O TRP D 569 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 576 through 579 Processing sheet with id=AF3, first strand: chain 'D' and resid 628 through 633 Processing sheet with id=AF4, first strand: chain 'D' and resid 662 through 670 removed outlier: 6.182A pdb=" N LEU D 659 " --> pdb=" O PRO D 663 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY D 693 " --> pdb=" O GLU D 725 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU D 725 " --> pdb=" O GLY D 693 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU D 695 " --> pdb=" O LEU D 723 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 717 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN D 703 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE D 715 " --> pdb=" O GLN D 703 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 740 through 743 removed outlier: 5.918A pdb=" N ASN D 760 " --> pdb=" O LEU D 766 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU D 766 " --> pdb=" O ASN D 760 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 777 through 784 removed outlier: 6.325A pdb=" N GLN D 888 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN D 886 " --> pdb=" O PRO D 780 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG D 782 " --> pdb=" O GLY D 884 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY D 884 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN D 784 " --> pdb=" O ARG D 882 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG D 882 " --> pdb=" O GLN D 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 883 " --> pdb=" O GLY D 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE D 990 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 12.043A pdb=" N ASP D 955 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP D 955 " --> pdb=" O GLN D1018 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN D1018 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N GLN D 957 " --> pdb=" O HIS D1016 " (cutoff:3.500A) removed outlier: 13.465A pdb=" N HIS D1016 " --> pdb=" O GLN D 957 " (cutoff:3.500A) removed outlier: 20.534A pdb=" N ASN D 959 " --> pdb=" O ARG D1014 " (cutoff:3.500A) removed outlier: 23.696A pdb=" N ARG D1014 " --> pdb=" O ASN D 959 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS D 845 " --> pdb=" O THR D 849 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA D 834 " --> pdb=" O THR D 830 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR D 830 " --> pdb=" O ALA D 834 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU D 836 " --> pdb=" O ALA D 828 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA D 828 " --> pdb=" O LEU D 836 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR D 838 " --> pdb=" O CYS D 826 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS D 826 " --> pdb=" O THR D 838 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA D 840 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 777 through 784 removed outlier: 6.325A pdb=" N GLN D 888 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN D 886 " --> pdb=" O PRO D 780 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG D 782 " --> pdb=" O GLY D 884 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY D 884 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN D 784 " --> pdb=" O ARG D 882 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG D 882 " --> pdb=" O GLN D 784 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 883 " --> pdb=" O GLY D 989 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE D 990 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 12.043A pdb=" N ASP D 955 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP D 952 " --> pdb=" O ASN D 946 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN D 946 " --> pdb=" O TRP D 952 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY D 954 " --> pdb=" O GLU D 944 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU D 944 " --> pdb=" O GLY D 954 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE D 958 " --> pdb=" O CYS D 940 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N CYS D 940 " --> pdb=" O PHE D 958 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR D 942 " --> pdb=" O LEU D 901 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU D 901 " --> pdb=" O THR D 942 " (cutoff:3.500A) 1268 hydrogen bonds defined for protein. 3288 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: 9.56 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8490 1.32 - 1.44: 7752 1.44 - 1.56: 17358 1.56 - 1.68: 0 1.68 - 1.81: 256 Bond restraints: 33856 Sorted by residual: bond pdb=" CA TYR C 539 " pdb=" C TYR C 539 " ideal model delta sigma weight residual 1.521 1.469 0.052 1.23e-02 6.61e+03 1.78e+01 bond pdb=" CA TYR B 539 " pdb=" C TYR B 539 " ideal model delta sigma weight residual 1.521 1.470 0.051 1.23e-02 6.61e+03 1.75e+01 bond pdb=" CA TYR D 539 " pdb=" C TYR D 539 " ideal model delta sigma weight residual 1.521 1.470 0.051 1.23e-02 6.61e+03 1.72e+01 bond pdb=" CA TYR A 539 " pdb=" C TYR A 539 " ideal model delta sigma weight residual 1.521 1.471 0.051 1.23e-02 6.61e+03 1.69e+01 bond pdb=" CA TYR C 553 " pdb=" C TYR C 553 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.60e+01 ... (remaining 33851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 42765 2.52 - 5.04: 2964 5.04 - 7.55: 333 7.55 - 10.07: 100 10.07 - 12.59: 30 Bond angle restraints: 46192 Sorted by residual: angle pdb=" C ARG D 532 " pdb=" N PRO D 533 " pdb=" CA PRO D 533 " ideal model delta sigma weight residual 120.31 126.67 -6.36 9.80e-01 1.04e+00 4.21e+01 angle pdb=" C ARG C 532 " pdb=" N PRO C 533 " pdb=" CA PRO C 533 " ideal model delta sigma weight residual 120.31 126.66 -6.35 9.80e-01 1.04e+00 4.20e+01 angle pdb=" C ARG B 532 " pdb=" N PRO B 533 " pdb=" CA PRO B 533 " ideal model delta sigma weight residual 120.31 126.65 -6.34 9.80e-01 1.04e+00 4.19e+01 angle pdb=" C ARG A 532 " pdb=" N PRO A 533 " pdb=" CA PRO A 533 " ideal model delta sigma weight residual 120.31 126.62 -6.31 9.80e-01 1.04e+00 4.15e+01 angle pdb=" C ASP C 803 " pdb=" N PRO C 804 " pdb=" CA PRO C 804 " ideal model delta sigma weight residual 119.84 127.89 -8.05 1.25e+00 6.40e-01 4.14e+01 ... (remaining 46187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 18820 17.81 - 35.63: 748 35.63 - 53.44: 136 53.44 - 71.26: 92 71.26 - 89.07: 60 Dihedral angle restraints: 19856 sinusoidal: 8016 harmonic: 11840 Sorted by residual: dihedral pdb=" CA LEU A 911 " pdb=" C LEU A 911 " pdb=" N THR A 912 " pdb=" CA THR A 912 " ideal model delta harmonic sigma weight residual -180.00 -159.34 -20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU B 911 " pdb=" C LEU B 911 " pdb=" N THR B 912 " pdb=" CA THR B 912 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU D 911 " pdb=" C LEU D 911 " pdb=" N THR D 912 " pdb=" CA THR D 912 " ideal model delta harmonic sigma weight residual -180.00 -159.36 -20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 19853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2250 0.055 - 0.109: 1864 0.109 - 0.164: 638 0.164 - 0.219: 72 0.219 - 0.273: 8 Chirality restraints: 4832 Sorted by residual: chirality pdb=" CA TRP D 554 " pdb=" N TRP D 554 " pdb=" C TRP D 554 " pdb=" CB TRP D 554 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA TRP A 554 " pdb=" N TRP A 554 " pdb=" C TRP A 554 " pdb=" CB TRP A 554 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA TRP B 554 " pdb=" N TRP B 554 " pdb=" C TRP B 554 " pdb=" CB TRP B 554 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 4829 not shown) Planarity restraints: 6100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 501 " -0.114 5.00e-02 4.00e+02 1.72e-01 4.73e+01 pdb=" N PRO C 502 " 0.297 5.00e-02 4.00e+02 pdb=" CA PRO C 502 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO C 502 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 501 " 0.114 5.00e-02 4.00e+02 1.72e-01 4.73e+01 pdb=" N PRO D 502 " -0.297 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 501 " -0.114 5.00e-02 4.00e+02 1.72e-01 4.73e+01 pdb=" N PRO B 502 " 0.297 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.088 5.00e-02 4.00e+02 ... (remaining 6097 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1189 2.67 - 3.23: 32290 3.23 - 3.79: 57525 3.79 - 4.34: 77794 4.34 - 4.90: 127486 Nonbonded interactions: 296284 Sorted by model distance: nonbonded pdb=" O ASP C 369 " pdb=" OD1 ASP C 369 " model vdw 2.116 3.040 nonbonded pdb=" O ASP A 369 " pdb=" OD1 ASP A 369 " model vdw 2.117 3.040 nonbonded pdb=" O ASP D 369 " pdb=" OD1 ASP D 369 " model vdw 2.117 3.040 nonbonded pdb=" O ASP B 369 " pdb=" OD1 ASP B 369 " model vdw 2.117 3.040 nonbonded pdb=" N GLN D 904 " pdb=" OE1 GLN D 904 " model vdw 2.136 3.120 ... (remaining 296279 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: 0.10 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 1.110 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 35.520 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.017 0.063 33860 Z= 1.075 Angle : 1.438 12.589 46200 Z= 0.904 Chirality : 0.076 0.273 4832 Planarity : 0.022 0.172 6100 Dihedral : 12.561 89.069 12220 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 2.13 % Allowed : 6.78 % Favored : 91.10 % Rotamer: Outliers : 0.23 % Allowed : 1.03 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: -1.87 (0.12), residues: 4088 helix: -1.91 (0.18), residues: 532 sheet: -0.31 (0.14), residues: 1352 loop : -1.68 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 562 TYR 0.058 0.007 TYR D 124 PHE 0.020 0.003 PHE B 990 TRP 0.073 0.006 TRP D 554 HIS 0.009 0.001 HIS A 991 Details of bonding type rmsd covalent geometry : bond 0.01707 (33856) covalent geometry : angle 1.43721 (46192) SS BOND : bond 0.00552 ( 4) SS BOND : angle 4.77549 ( 8) hydrogen bonds : bond 0.15155 ( 1212) hydrogen bonds : angle 7.46175 ( 3288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 793 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: -0.0456 (tpt) cc_final: -0.0901 (ttm) REVERT: A 3 MET cc_start: 0.2106 (mmm) cc_final: 0.1417 (tpt) REVERT: A 31 HIS cc_start: 0.8054 (p90) cc_final: 0.7835 (p-80) REVERT: A 41 GLU cc_start: 0.7160 (tp30) cc_final: 0.6239 (tm-30) REVERT: A 42 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6281 (tt0) REVERT: A 58 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7317 (mp0) REVERT: A 72 GLU cc_start: 0.6993 (mp0) cc_final: 0.6612 (mm-30) REVERT: A 86 VAL cc_start: 0.7926 (t) cc_final: 0.7520 (p) REVERT: A 129 ASN cc_start: 0.7218 (m-40) cc_final: 0.6895 (t0) REVERT: A 137 GLU cc_start: 0.6492 (pt0) cc_final: 0.5925 (pm20) REVERT: A 242 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7099 (tt0) REVERT: A 244 GLU cc_start: 0.7569 (tt0) cc_final: 0.7167 (tp30) REVERT: A 246 GLN cc_start: 0.7013 (tt0) cc_final: 0.6693 (mt0) REVERT: A 252 ARG cc_start: 0.6458 (mmm-85) cc_final: 0.5939 (mmt180) REVERT: A 253 ASP cc_start: 0.6719 (m-30) cc_final: 0.6270 (p0) REVERT: A 254 TYR cc_start: 0.6961 (p90) cc_final: 0.6547 (p90) REVERT: A 293 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7494 (mpt180) REVERT: A 297 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6287 (tp30) REVERT: A 329 CYS cc_start: 0.7554 (t) cc_final: 0.7182 (p) REVERT: A 335 GLU cc_start: 0.8329 (tt0) cc_final: 0.7398 (tm-30) REVERT: A 363 LEU cc_start: 0.7164 (mt) cc_final: 0.6897 (mm) REVERT: A 371 GLN cc_start: 0.7196 (tp40) cc_final: 0.6885 (mp10) REVERT: A 405 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7423 (ttp80) REVERT: A 432 ARG cc_start: 0.7057 (mtm180) cc_final: 0.6795 (mtp85) REVERT: A 439 GLU cc_start: 0.7473 (tt0) cc_final: 0.7169 (mp0) REVERT: A 443 ARG cc_start: 0.7327 (mtp85) cc_final: 0.6988 (mtp-110) REVERT: A 488 GLU cc_start: 0.7101 (pm20) cc_final: 0.6629 (tm-30) REVERT: A 503 MET cc_start: 0.8137 (mtm) cc_final: 0.7869 (mtp) REVERT: A 552 LYS cc_start: 0.8031 (mttt) cc_final: 0.7829 (mtpm) REVERT: A 662 LYS cc_start: 0.6817 (tttt) cc_final: 0.6568 (mtmm) REVERT: A 746 MET cc_start: 0.6878 (mmm) cc_final: 0.6420 (mmm) REVERT: A 749 CYS cc_start: 0.7141 (t) cc_final: 0.6697 (t) REVERT: A 751 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6586 (mp0) REVERT: A 754 ASN cc_start: 0.6715 (p0) cc_final: 0.6190 (p0) REVERT: A 756 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6746 (mtp180) REVERT: A 758 GLN cc_start: 0.8081 (tt0) cc_final: 0.7866 (tt0) REVERT: A 760 ASN cc_start: 0.7882 (t0) cc_final: 0.7447 (t0) REVERT: A 761 ARG cc_start: 0.7637 (ttt180) cc_final: 0.7278 (ttp80) REVERT: A 769 MET cc_start: 0.7270 (ttt) cc_final: 0.6544 (tmt) REVERT: A 774 LYS cc_start: 0.6822 (tttt) cc_final: 0.6341 (tttt) REVERT: A 782 ARG cc_start: 0.7939 (mtm180) cc_final: 0.7566 (mtp180) REVERT: A 784 GLN cc_start: 0.7809 (tp40) cc_final: 0.7520 (tt0) REVERT: A 858 ARG cc_start: 0.8235 (ttt-90) cc_final: 0.7987 (ttt90) REVERT: A 966 GLN cc_start: 0.7748 (tt0) cc_final: 0.7543 (tt0) REVERT: A 970 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6894 (mp0) REVERT: A 978 HIS cc_start: 0.6286 (m-70) cc_final: 0.5927 (p-80) REVERT: A 997 ASP cc_start: 0.7410 (m-30) cc_final: 0.7037 (m-30) REVERT: A 1005 SER cc_start: 0.7409 (m) cc_final: 0.7040 (p) REVERT: A 1014 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7339 (mtm-85) REVERT: B 3 MET cc_start: 0.2049 (mmm) cc_final: 0.1422 (tpt) REVERT: B 41 GLU cc_start: 0.7101 (tp30) cc_final: 0.6293 (tm-30) REVERT: B 42 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6187 (tt0) REVERT: B 86 VAL cc_start: 0.7808 (t) cc_final: 0.7366 (p) REVERT: B 203 MET cc_start: 0.7752 (ptt) cc_final: 0.7543 (ptt) REVERT: B 242 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6937 (tt0) REVERT: B 244 GLU cc_start: 0.7481 (tt0) cc_final: 0.7261 (tt0) REVERT: B 246 GLN cc_start: 0.7004 (tt0) cc_final: 0.6711 (mt0) REVERT: B 252 ARG cc_start: 0.6539 (mmm-85) cc_final: 0.5982 (mmt180) REVERT: B 253 ASP cc_start: 0.6608 (m-30) cc_final: 0.6204 (p0) REVERT: B 254 TYR cc_start: 0.6797 (p90) cc_final: 0.6493 (p90) REVERT: B 293 ARG cc_start: 0.7749 (mtt90) cc_final: 0.7498 (mpt180) REVERT: B 297 GLU cc_start: 0.6745 (mm-30) cc_final: 0.5815 (mp0) REVERT: B 329 CYS cc_start: 0.7478 (t) cc_final: 0.7150 (p) REVERT: B 335 GLU cc_start: 0.8311 (tt0) cc_final: 0.8011 (tt0) REVERT: B 371 GLN cc_start: 0.7066 (tp40) cc_final: 0.6537 (mp10) REVERT: B 432 ARG cc_start: 0.7041 (mtm180) cc_final: 0.6826 (mtp85) REVERT: B 439 GLU cc_start: 0.7571 (tt0) cc_final: 0.7249 (mp0) REVERT: B 443 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6916 (mtp-110) REVERT: B 488 GLU cc_start: 0.7045 (pm20) cc_final: 0.6554 (tm-30) REVERT: B 503 MET cc_start: 0.8172 (mtm) cc_final: 0.7896 (mtp) REVERT: B 552 LYS cc_start: 0.8069 (mttt) cc_final: 0.7855 (mtpm) REVERT: B 682 GLU cc_start: 0.6767 (tt0) cc_final: 0.6531 (tm-30) REVERT: B 746 MET cc_start: 0.6836 (mmm) cc_final: 0.6563 (mmp) REVERT: B 751 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6549 (mp0) REVERT: B 756 ARG cc_start: 0.7091 (ttm110) cc_final: 0.6565 (mtp180) REVERT: B 761 ARG cc_start: 0.7574 (ttt180) cc_final: 0.7216 (ttp80) REVERT: B 762 GLN cc_start: 0.6867 (mm-40) cc_final: 0.6623 (tm-30) REVERT: B 769 MET cc_start: 0.7324 (ttt) cc_final: 0.6751 (tmt) REVERT: B 771 ILE cc_start: 0.8344 (mt) cc_final: 0.8143 (mt) REVERT: B 774 LYS cc_start: 0.6354 (tttt) cc_final: 0.5912 (tttt) REVERT: B 775 LYS cc_start: 0.7840 (mttt) cc_final: 0.7503 (mttp) REVERT: B 782 ARG cc_start: 0.8062 (mtm180) cc_final: 0.7646 (mtp180) REVERT: B 784 GLN cc_start: 0.7682 (tp40) cc_final: 0.7451 (tt0) REVERT: B 805 ASN cc_start: 0.7321 (m-40) cc_final: 0.6975 (m-40) REVERT: B 812 LYS cc_start: 0.7671 (mttt) cc_final: 0.7467 (mttm) REVERT: B 838 THR cc_start: 0.8230 (m) cc_final: 0.7680 (p) REVERT: B 966 GLN cc_start: 0.7633 (tt0) cc_final: 0.7421 (tt0) REVERT: B 970 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6795 (mp0) REVERT: B 978 HIS cc_start: 0.6075 (m-70) cc_final: 0.5533 (p-80) REVERT: B 1005 SER cc_start: 0.7490 (m) cc_final: 0.7166 (p) REVERT: B 1014 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7126 (mtm-85) REVERT: C 1 MET cc_start: -0.0401 (tpt) cc_final: -0.1106 (ttm) REVERT: C 3 MET cc_start: 0.1991 (mmm) cc_final: 0.1398 (tpt) REVERT: C 41 GLU cc_start: 0.6690 (tp30) cc_final: 0.5878 (tm-30) REVERT: C 42 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6443 (mm-30) REVERT: C 50 GLN cc_start: 0.7315 (mm-40) cc_final: 0.7061 (mm110) REVERT: C 86 VAL cc_start: 0.7655 (t) cc_final: 0.7276 (p) REVERT: C 102 THR cc_start: 0.7428 (p) cc_final: 0.7035 (t) REVERT: C 242 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6859 (tt0) REVERT: C 244 GLU cc_start: 0.7352 (tt0) cc_final: 0.7083 (tp30) REVERT: C 246 GLN cc_start: 0.6894 (tt0) cc_final: 0.6614 (mt0) REVERT: C 253 ASP cc_start: 0.6439 (m-30) cc_final: 0.6028 (p0) REVERT: C 254 TYR cc_start: 0.6408 (p90) cc_final: 0.6178 (p90) REVERT: C 297 GLU cc_start: 0.6475 (mm-30) cc_final: 0.5548 (mp0) REVERT: C 335 GLU cc_start: 0.8049 (tt0) cc_final: 0.7790 (tt0) REVERT: C 371 GLN cc_start: 0.6960 (tp40) cc_final: 0.6521 (mp10) REVERT: C 432 ARG cc_start: 0.7043 (mtm180) cc_final: 0.6780 (mtp85) REVERT: C 439 GLU cc_start: 0.7483 (tt0) cc_final: 0.7126 (mp0) REVERT: C 488 GLU cc_start: 0.6926 (pm20) cc_final: 0.6563 (tm-30) REVERT: C 631 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7293 (ttp80) REVERT: C 656 MET cc_start: 0.7939 (mtm) cc_final: 0.7702 (mtt) REVERT: C 660 ASP cc_start: 0.6822 (m-30) cc_final: 0.6458 (m-30) REVERT: C 668 GLU cc_start: 0.7659 (tt0) cc_final: 0.7338 (tt0) REVERT: C 762 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6759 (mm110) REVERT: C 769 MET cc_start: 0.6981 (ttt) cc_final: 0.6771 (tmm) REVERT: C 775 LYS cc_start: 0.7578 (mttt) cc_final: 0.7275 (mttp) REVERT: C 782 ARG cc_start: 0.7611 (mtm180) cc_final: 0.7401 (mtp-110) REVERT: C 812 LYS cc_start: 0.7752 (mttt) cc_final: 0.7522 (mttm) REVERT: C 894 GLU cc_start: 0.6728 (tp30) cc_final: 0.6462 (mp0) REVERT: C 955 ASP cc_start: 0.7042 (t0) cc_final: 0.6759 (t70) REVERT: C 966 GLN cc_start: 0.7645 (tt0) cc_final: 0.7317 (tt0) REVERT: C 970 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6615 (mm-30) REVERT: C 978 HIS cc_start: 0.5640 (m-70) cc_final: 0.5079 (p90) REVERT: C 997 ASP cc_start: 0.7311 (m-30) cc_final: 0.6947 (m-30) REVERT: C 1005 SER cc_start: 0.7495 (m) cc_final: 0.7174 (p) REVERT: C 1014 ARG cc_start: 0.7675 (mtp85) cc_final: 0.7106 (mtm-85) REVERT: D 1 MET cc_start: -0.0693 (tpt) cc_final: -0.1082 (ttm) REVERT: D 3 MET cc_start: 0.2100 (mmm) cc_final: 0.1636 (tpt) REVERT: D 41 GLU cc_start: 0.6891 (tp30) cc_final: 0.5976 (tm-30) REVERT: D 42 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6203 (tt0) REVERT: D 50 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7198 (mm110) REVERT: D 72 GLU cc_start: 0.7079 (mp0) cc_final: 0.6857 (mm-30) REVERT: D 86 VAL cc_start: 0.7609 (t) cc_final: 0.7229 (p) REVERT: D 102 THR cc_start: 0.7416 (p) cc_final: 0.7075 (t) REVERT: D 203 MET cc_start: 0.7292 (ptt) cc_final: 0.7084 (ptt) REVERT: D 242 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6782 (tt0) REVERT: D 244 GLU cc_start: 0.7520 (tt0) cc_final: 0.7248 (tt0) REVERT: D 252 ARG cc_start: 0.6414 (mmm-85) cc_final: 0.5878 (mmt180) REVERT: D 253 ASP cc_start: 0.6578 (m-30) cc_final: 0.6137 (p0) REVERT: D 254 TYR cc_start: 0.6741 (p90) cc_final: 0.6339 (p90) REVERT: D 293 ARG cc_start: 0.7615 (mtt90) cc_final: 0.7286 (mpt180) REVERT: D 297 GLU cc_start: 0.6549 (mm-30) cc_final: 0.5527 (mp0) REVERT: D 335 GLU cc_start: 0.8077 (tt0) cc_final: 0.7823 (tt0) REVERT: D 370 GLU cc_start: 0.7225 (tt0) cc_final: 0.7023 (tp30) REVERT: D 371 GLN cc_start: 0.6945 (tp40) cc_final: 0.6497 (mp10) REVERT: D 421 MET cc_start: 0.7602 (mmm) cc_final: 0.7359 (mmm) REVERT: D 432 ARG cc_start: 0.7287 (mtm180) cc_final: 0.6951 (mtp85) REVERT: D 443 ARG cc_start: 0.7153 (mtp85) cc_final: 0.6882 (mtp-110) REVERT: D 488 GLU cc_start: 0.6910 (pm20) cc_final: 0.6597 (tm-30) REVERT: D 503 MET cc_start: 0.7946 (mtm) cc_final: 0.7719 (mtp) REVERT: D 656 MET cc_start: 0.7749 (mtm) cc_final: 0.7498 (mtt) REVERT: D 662 LYS cc_start: 0.7022 (tttt) cc_final: 0.6616 (mtmm) REVERT: D 668 GLU cc_start: 0.7512 (tt0) cc_final: 0.7279 (tt0) REVERT: D 769 MET cc_start: 0.7119 (ttt) cc_final: 0.6634 (tmt) REVERT: D 775 LYS cc_start: 0.7815 (mttt) cc_final: 0.7564 (mttm) REVERT: D 782 ARG cc_start: 0.7422 (mtm180) cc_final: 0.7186 (mtp-110) REVERT: D 868 THR cc_start: 0.8197 (m) cc_final: 0.7955 (m) REVERT: D 894 GLU cc_start: 0.6808 (tp30) cc_final: 0.6572 (mp0) REVERT: D 966 GLN cc_start: 0.7489 (tt0) cc_final: 0.7180 (tt0) REVERT: D 970 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6777 (mm-30) REVERT: D 1005 SER cc_start: 0.7535 (m) cc_final: 0.7323 (p) REVERT: D 1014 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7097 (mtm-85) outliers start: 8 outliers final: 8 residues processed: 801 average time/residue: 0.9257 time to fit residues: 852.2997 Evaluate side-chains 516 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 508 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 PRO Chi-restraints excluded: chain A residue 561 PRO Chi-restraints excluded: chain B residue 435 PRO Chi-restraints excluded: chain B residue 561 PRO Chi-restraints excluded: chain C residue 435 PRO Chi-restraints excluded: chain C residue 561 PRO Chi-restraints excluded: chain D residue 435 PRO Chi-restraints excluded: chain D residue 561 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 366 GLN A 396 HIS A 419 HIS A 511 GLN A 647 HIS A 654 HIS A 825 GLN ** A 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 HIS A 959 ASN B 94 HIS B 366 GLN B 396 HIS B 419 HIS B 647 HIS B 654 HIS B 726 ASN B 825 GLN ** B 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 GLN C 94 HIS C 295 ASN C 396 HIS C 419 HIS C 647 HIS C 845 HIS C 959 ASN D 39 ASN D 94 HIS D 246 GLN D 267 GLN D 396 HIS D 419 HIS D 647 HIS D 740 HIS D 762 GLN D 784 GLN D 959 ASN D 986 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123878 restraints weight = 29712.149| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.14 r_work: 0.3271 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 33860 Z= 0.206 Angle : 0.687 8.467 46200 Z= 0.373 Chirality : 0.048 0.189 4832 Planarity : 0.009 0.071 6100 Dihedral : 5.985 77.750 4508 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.57 % Allowed : 6.16 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: -0.71 (0.12), residues: 4088 helix: -0.33 (0.19), residues: 548 sheet: 0.23 (0.14), residues: 1308 loop : -0.91 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 449 TYR 0.019 0.003 TYR C 101 PHE 0.014 0.002 PHE D 990 TRP 0.042 0.002 TRP B 554 HIS 0.007 0.002 HIS C 647 Details of bonding type rmsd covalent geometry : bond 0.00454 (33856) covalent geometry : angle 0.68235 (46192) SS BOND : bond 0.00474 ( 4) SS BOND : angle 6.35584 ( 8) hydrogen bonds : bond 0.05115 ( 1212) hydrogen bonds : angle 5.71983 ( 3288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 585 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7767 (tp30) cc_final: 0.7457 (tm-30) REVERT: A 78 ASP cc_start: 0.7782 (m-30) cc_final: 0.7548 (m-30) REVERT: A 220 THR cc_start: 0.8204 (p) cc_final: 0.7942 (t) REVERT: A 297 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7132 (mm-30) REVERT: A 335 GLU cc_start: 0.8804 (tt0) cc_final: 0.8479 (tm-30) REVERT: A 359 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: A 746 MET cc_start: 0.7229 (mmm) cc_final: 0.7010 (mmp) REVERT: A 747 ASP cc_start: 0.7016 (p0) cc_final: 0.6588 (m-30) REVERT: A 756 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7461 (mtp180) REVERT: A 769 MET cc_start: 0.7978 (ttt) cc_final: 0.7585 (tmt) REVERT: B 41 GLU cc_start: 0.7789 (tp30) cc_final: 0.7312 (tm-30) REVERT: B 220 THR cc_start: 0.8303 (p) cc_final: 0.8011 (t) REVERT: B 293 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7893 (mpt180) REVERT: B 297 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 335 GLU cc_start: 0.8794 (tt0) cc_final: 0.8477 (tm-30) REVERT: B 363 LEU cc_start: 0.8557 (mt) cc_final: 0.8279 (mm) REVERT: B 405 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8544 (ttp-110) REVERT: B 746 MET cc_start: 0.7215 (mmm) cc_final: 0.6970 (mmp) REVERT: B 756 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7495 (mtp180) REVERT: B 769 MET cc_start: 0.7961 (ttt) cc_final: 0.7656 (tmt) REVERT: C 1 MET cc_start: -0.0216 (tpt) cc_final: -0.0541 (ttm) REVERT: C 41 GLU cc_start: 0.7708 (tp30) cc_final: 0.7391 (tm-30) REVERT: C 42 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7683 (tt0) REVERT: C 50 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7734 (mm110) REVERT: C 129 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7546 (t0) REVERT: C 254 TYR cc_start: 0.7596 (p90) cc_final: 0.7350 (p90) REVERT: C 335 GLU cc_start: 0.8763 (tt0) cc_final: 0.8403 (tm-30) REVERT: C 584 ASN cc_start: 0.7904 (m110) cc_final: 0.7385 (m-40) REVERT: C 747 ASP cc_start: 0.7275 (p0) cc_final: 0.6353 (m-30) REVERT: C 762 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7226 (mm110) REVERT: C 769 MET cc_start: 0.7959 (ttt) cc_final: 0.7686 (tmt) REVERT: C 774 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7292 (ttmt) REVERT: D 41 GLU cc_start: 0.7675 (tp30) cc_final: 0.7216 (tm-30) REVERT: D 42 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7517 (tt0) REVERT: D 50 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7774 (mm110) REVERT: D 220 THR cc_start: 0.8259 (p) cc_final: 0.8043 (t) REVERT: D 238 ARG cc_start: 0.8388 (mtp85) cc_final: 0.8008 (mtm110) REVERT: D 293 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7827 (mpt180) REVERT: D 297 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7172 (mm-30) REVERT: D 335 GLU cc_start: 0.8739 (tt0) cc_final: 0.8387 (tm-30) REVERT: D 751 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7013 (mp0) REVERT: D 769 MET cc_start: 0.7928 (ttt) cc_final: 0.7511 (tmt) REVERT: D 774 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7615 (mtpp) REVERT: D 925 ASP cc_start: 0.7990 (m-30) cc_final: 0.7731 (t70) outliers start: 55 outliers final: 16 residues processed: 610 average time/residue: 0.9063 time to fit residues: 638.4221 Evaluate side-chains 487 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 468 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 886 ASN Chi-restraints excluded: chain C residue 1018 GLN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 516 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 223 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 386 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 100 optimal weight: 0.0040 chunk 56 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 315 optimal weight: 6.9990 chunk 302 optimal weight: 0.8980 chunk 390 optimal weight: 8.9990 overall best weight: 3.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 267 GLN A 758 GLN A 784 GLN A 864 GLN A 959 ASN B 246 GLN B 584 ASN B 726 ASN B 762 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 647 HIS C 654 HIS C 864 GLN C 886 ASN C 950 HIS C 959 ASN D 584 ASN D 647 HIS D 654 HIS D 762 GLN D 950 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120812 restraints weight = 29917.557| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.10 r_work: 0.3226 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33860 Z= 0.194 Angle : 0.651 9.071 46200 Z= 0.349 Chirality : 0.046 0.170 4832 Planarity : 0.005 0.052 6100 Dihedral : 5.852 75.254 4484 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 1.68 % Allowed : 9.47 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: -0.09 (0.13), residues: 4088 helix: 0.16 (0.21), residues: 540 sheet: 0.46 (0.14), residues: 1340 loop : -0.38 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 449 TYR 0.019 0.002 TYR D 101 PHE 0.012 0.002 PHE A1008 TRP 0.040 0.002 TRP C 554 HIS 0.011 0.002 HIS B 978 Details of bonding type rmsd covalent geometry : bond 0.00419 (33856) covalent geometry : angle 0.64491 (46192) SS BOND : bond 0.01239 ( 4) SS BOND : angle 6.96966 ( 8) hydrogen bonds : bond 0.05225 ( 1212) hydrogen bonds : angle 5.54478 ( 3288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 467 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2145 (OUTLIER) cc_final: 0.1910 (ttp) REVERT: A 41 GLU cc_start: 0.7819 (tp30) cc_final: 0.7502 (tm-30) REVERT: A 58 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: A 78 ASP cc_start: 0.7835 (m-30) cc_final: 0.7593 (m-30) REVERT: A 220 THR cc_start: 0.8324 (p) cc_final: 0.8030 (t) REVERT: A 297 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7142 (mm-30) REVERT: A 335 GLU cc_start: 0.8820 (tt0) cc_final: 0.8517 (tm-30) REVERT: A 756 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7542 (mtp180) REVERT: A 769 MET cc_start: 0.7954 (ttt) cc_final: 0.7532 (tmt) REVERT: A 774 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7601 (tttt) REVERT: A 970 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: B 41 GLU cc_start: 0.7852 (tp30) cc_final: 0.7483 (tm-30) REVERT: B 220 THR cc_start: 0.8336 (p) cc_final: 0.8023 (t) REVERT: B 252 ARG cc_start: 0.7152 (mmt180) cc_final: 0.6933 (mmm160) REVERT: B 293 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7845 (mpt180) REVERT: B 297 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7164 (mm-30) REVERT: B 335 GLU cc_start: 0.8809 (tt0) cc_final: 0.8510 (tm-30) REVERT: B 363 LEU cc_start: 0.8637 (mt) cc_final: 0.8361 (mm) REVERT: B 756 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7410 (mtp180) REVERT: B 769 MET cc_start: 0.8013 (ttt) cc_final: 0.7583 (tmt) REVERT: B 970 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: C 1 MET cc_start: 0.0005 (tpt) cc_final: -0.0316 (ttm) REVERT: C 3 MET cc_start: 0.1019 (mmp) cc_final: 0.0761 (mmt) REVERT: C 41 GLU cc_start: 0.7732 (tp30) cc_final: 0.7368 (tm-30) REVERT: C 42 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7685 (tt0) REVERT: C 50 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7712 (mm110) REVERT: C 129 ASN cc_start: 0.8156 (t0) cc_final: 0.7786 (t0) REVERT: C 252 ARG cc_start: 0.7094 (mmt180) cc_final: 0.6844 (mmm160) REVERT: C 254 TYR cc_start: 0.7682 (p90) cc_final: 0.7410 (p90) REVERT: C 335 GLU cc_start: 0.8784 (tt0) cc_final: 0.8463 (tm-30) REVERT: C 370 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: C 769 MET cc_start: 0.7978 (ttt) cc_final: 0.7525 (tmt) REVERT: C 774 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7545 (tttt) REVERT: C 970 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: D 41 GLU cc_start: 0.7781 (tp30) cc_final: 0.7398 (tm-30) REVERT: D 50 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7788 (mm110) REVERT: D 220 THR cc_start: 0.8310 (p) cc_final: 0.8039 (t) REVERT: D 254 TYR cc_start: 0.7777 (p90) cc_final: 0.7456 (p90) REVERT: D 293 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7823 (mpt180) REVERT: D 335 GLU cc_start: 0.8797 (tt0) cc_final: 0.8476 (tm-30) REVERT: D 359 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: D 369 ASP cc_start: 0.8212 (p0) cc_final: 0.7860 (p0) REVERT: D 751 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7219 (mp0) REVERT: D 769 MET cc_start: 0.7941 (ttt) cc_final: 0.7483 (tmt) REVERT: D 774 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7751 (mtpp) REVERT: D 970 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7279 (mp0) outliers start: 59 outliers final: 22 residues processed: 507 average time/residue: 0.8679 time to fit residues: 509.2877 Evaluate side-chains 467 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 437 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain B residue 970 GLU Chi-restraints excluded: chain B residue 1001 SER Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 1001 SER Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 924 SER Chi-restraints excluded: chain D residue 970 GLU Chi-restraints excluded: chain D residue 1001 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 355 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 372 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 chunk 387 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 HIS A 605 ASN B 94 HIS B 267 GLN B 584 ASN B 605 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN ** B 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 ASN C 959 ASN D 584 ASN D 605 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121131 restraints weight = 29519.596| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.07 r_work: 0.3230 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33860 Z= 0.188 Angle : 0.628 9.361 46200 Z= 0.335 Chirality : 0.046 0.175 4832 Planarity : 0.004 0.041 6100 Dihedral : 5.741 69.710 4484 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.31 % Rotamer: Outliers : 1.91 % Allowed : 10.02 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.09 (0.13), residues: 4088 helix: 0.20 (0.21), residues: 552 sheet: 0.58 (0.14), residues: 1328 loop : -0.23 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 447 TYR 0.019 0.002 TYR D 101 PHE 0.010 0.002 PHE C 275 TRP 0.041 0.002 TRP D 554 HIS 0.010 0.001 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00401 (33856) covalent geometry : angle 0.62448 (46192) SS BOND : bond 0.01335 ( 4) SS BOND : angle 5.11287 ( 8) hydrogen bonds : bond 0.05013 ( 1212) hydrogen bonds : angle 5.46110 ( 3288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 455 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7842 (tp30) cc_final: 0.7576 (tm-30) REVERT: A 58 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: A 78 ASP cc_start: 0.7824 (m-30) cc_final: 0.7622 (m-30) REVERT: A 129 ASN cc_start: 0.8174 (t0) cc_final: 0.7815 (t0) REVERT: A 206 MET cc_start: 0.8820 (mtm) cc_final: 0.8534 (mtt) REVERT: A 220 THR cc_start: 0.8339 (p) cc_final: 0.8039 (t) REVERT: A 254 TYR cc_start: 0.7766 (p90) cc_final: 0.7457 (p90) REVERT: A 297 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 335 GLU cc_start: 0.8805 (tt0) cc_final: 0.8512 (tm-30) REVERT: A 359 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: A 756 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7498 (mtp180) REVERT: A 769 MET cc_start: 0.7894 (ttt) cc_final: 0.7401 (tmt) REVERT: A 774 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7594 (tttt) REVERT: A 970 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: B 41 GLU cc_start: 0.7842 (tp30) cc_final: 0.7502 (tm-30) REVERT: B 129 ASN cc_start: 0.8211 (t0) cc_final: 0.7845 (t0) REVERT: B 220 THR cc_start: 0.8320 (p) cc_final: 0.8008 (t) REVERT: B 254 TYR cc_start: 0.7747 (p90) cc_final: 0.7383 (p90) REVERT: B 297 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7148 (mm-30) REVERT: B 335 GLU cc_start: 0.8778 (tt0) cc_final: 0.8469 (tm-30) REVERT: B 756 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7487 (mtp180) REVERT: B 769 MET cc_start: 0.7882 (ttt) cc_final: 0.7445 (tmt) REVERT: B 970 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: C 41 GLU cc_start: 0.7749 (tp30) cc_final: 0.7414 (tm-30) REVERT: C 50 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7611 (mm110) REVERT: C 129 ASN cc_start: 0.8155 (t0) cc_final: 0.7814 (t0) REVERT: C 212 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7116 (t0) REVERT: C 254 TYR cc_start: 0.7682 (p90) cc_final: 0.7379 (p90) REVERT: C 335 GLU cc_start: 0.8770 (tt0) cc_final: 0.8469 (tm-30) REVERT: C 370 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7257 (tp30) REVERT: C 769 MET cc_start: 0.7896 (ttt) cc_final: 0.7423 (tmt) REVERT: C 774 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7619 (tttt) REVERT: C 970 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: D 41 GLU cc_start: 0.7838 (tp30) cc_final: 0.7504 (tm-30) REVERT: D 50 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7786 (mm110) REVERT: D 129 ASN cc_start: 0.8241 (t0) cc_final: 0.7860 (t0) REVERT: D 220 THR cc_start: 0.8332 (p) cc_final: 0.8046 (t) REVERT: D 254 TYR cc_start: 0.7710 (p90) cc_final: 0.7460 (p90) REVERT: D 335 GLU cc_start: 0.8776 (tt0) cc_final: 0.8484 (tm-30) REVERT: D 359 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: D 369 ASP cc_start: 0.8152 (p0) cc_final: 0.7858 (p0) REVERT: D 751 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7362 (mp0) REVERT: D 769 MET cc_start: 0.7848 (ttt) cc_final: 0.7337 (tmt) REVERT: D 774 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7649 (tttt) REVERT: D 970 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7133 (mp0) outliers start: 67 outliers final: 28 residues processed: 494 average time/residue: 0.9078 time to fit residues: 519.3607 Evaluate side-chains 471 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 434 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain B residue 970 GLU Chi-restraints excluded: chain B residue 1001 SER Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 1001 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 924 SER Chi-restraints excluded: chain D residue 970 GLU Chi-restraints excluded: chain D residue 1001 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 316 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 369 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 379 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 726 ASN B 584 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 959 ASN D 584 ASN D 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119384 restraints weight = 29557.258| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.12 r_work: 0.3201 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 33860 Z= 0.201 Angle : 0.652 9.372 46200 Z= 0.346 Chirality : 0.046 0.177 4832 Planarity : 0.004 0.037 6100 Dihedral : 5.751 65.169 4484 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.26 % Rotamer: Outliers : 1.88 % Allowed : 10.73 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.17 (0.13), residues: 4088 helix: 0.22 (0.21), residues: 552 sheet: 0.67 (0.14), residues: 1328 loop : -0.19 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 293 TYR 0.019 0.002 TYR D 101 PHE 0.011 0.002 PHE C 275 TRP 0.041 0.002 TRP D 554 HIS 0.007 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00437 (33856) covalent geometry : angle 0.64449 (46192) SS BOND : bond 0.01601 ( 4) SS BOND : angle 7.60209 ( 8) hydrogen bonds : bond 0.05084 ( 1212) hydrogen bonds : angle 5.45774 ( 3288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 437 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7860 (tp30) cc_final: 0.7552 (tm-30) REVERT: A 77 CYS cc_start: 0.7664 (p) cc_final: 0.7191 (m) REVERT: A 129 ASN cc_start: 0.8176 (t0) cc_final: 0.7839 (t0) REVERT: A 220 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8066 (t) REVERT: A 254 TYR cc_start: 0.7781 (p90) cc_final: 0.7445 (p90) REVERT: A 297 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 335 GLU cc_start: 0.8804 (tt0) cc_final: 0.8514 (tm-30) REVERT: A 359 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: A 756 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7426 (mtp180) REVERT: A 769 MET cc_start: 0.7921 (ttt) cc_final: 0.7361 (tmt) REVERT: A 774 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7606 (tttt) REVERT: A 970 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: B 41 GLU cc_start: 0.7861 (tp30) cc_final: 0.7488 (tm-30) REVERT: B 76 GLU cc_start: 0.7281 (pp20) cc_final: 0.7078 (pp20) REVERT: B 129 ASN cc_start: 0.8207 (t0) cc_final: 0.7853 (t0) REVERT: B 220 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8031 (t) REVERT: B 254 TYR cc_start: 0.7734 (p90) cc_final: 0.7370 (p90) REVERT: B 297 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7151 (mm-30) REVERT: B 335 GLU cc_start: 0.8748 (tt0) cc_final: 0.8454 (tm-30) REVERT: B 359 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: B 756 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7442 (mtp180) REVERT: B 769 MET cc_start: 0.7926 (ttt) cc_final: 0.7408 (tmt) REVERT: B 970 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: C 41 GLU cc_start: 0.7826 (tp30) cc_final: 0.7447 (tm-30) REVERT: C 50 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7574 (mm110) REVERT: C 76 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7583 (pp20) REVERT: C 129 ASN cc_start: 0.8146 (t0) cc_final: 0.7809 (t0) REVERT: C 212 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7101 (t0) REVERT: C 254 TYR cc_start: 0.7726 (p90) cc_final: 0.7417 (p90) REVERT: C 335 GLU cc_start: 0.8760 (tt0) cc_final: 0.8480 (tm-30) REVERT: C 370 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7278 (tp30) REVERT: C 547 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8992 (mp) REVERT: C 769 MET cc_start: 0.7867 (ttt) cc_final: 0.7336 (tmt) REVERT: C 774 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7637 (tttt) REVERT: C 970 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: D 41 GLU cc_start: 0.7873 (tp30) cc_final: 0.7487 (tm-30) REVERT: D 50 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7682 (mm110) REVERT: D 129 ASN cc_start: 0.8200 (t0) cc_final: 0.7811 (t0) REVERT: D 220 THR cc_start: 0.8338 (p) cc_final: 0.8050 (t) REVERT: D 254 TYR cc_start: 0.7732 (p90) cc_final: 0.7475 (p90) REVERT: D 335 GLU cc_start: 0.8777 (tt0) cc_final: 0.8486 (tm-30) REVERT: D 359 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: D 369 ASP cc_start: 0.8126 (p0) cc_final: 0.7834 (p0) REVERT: D 547 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8967 (mp) REVERT: D 751 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7462 (mp0) REVERT: D 769 MET cc_start: 0.7835 (ttt) cc_final: 0.7296 (tmt) REVERT: D 774 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7689 (tttt) REVERT: D 970 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7136 (mp0) outliers start: 66 outliers final: 29 residues processed: 480 average time/residue: 0.8864 time to fit residues: 492.8607 Evaluate side-chains 475 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 433 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 970 GLU Chi-restraints excluded: chain B residue 1001 SER Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 1001 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 924 SER Chi-restraints excluded: chain D residue 970 GLU Chi-restraints excluded: chain D residue 1001 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 91 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 392 optimal weight: 6.9990 chunk 313 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 605 ASN B 227 HIS B 584 ASN B 605 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 HIS C 605 ASN C 959 ASN D 584 ASN D 605 ASN D 762 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.141937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118063 restraints weight = 29508.515| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.10 r_work: 0.3180 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 33860 Z= 0.256 Angle : 0.705 14.083 46200 Z= 0.376 Chirality : 0.049 0.187 4832 Planarity : 0.005 0.035 6100 Dihedral : 5.891 58.440 4484 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 2.23 % Allowed : 11.10 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.14 (0.13), residues: 4088 helix: 0.15 (0.21), residues: 544 sheet: 0.64 (0.14), residues: 1356 loop : -0.19 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 293 TYR 0.021 0.002 TYR D 101 PHE 0.013 0.002 PHE C 275 TRP 0.044 0.002 TRP D 554 HIS 0.009 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00557 (33856) covalent geometry : angle 0.69682 (46192) SS BOND : bond 0.01932 ( 4) SS BOND : angle 8.40734 ( 8) hydrogen bonds : bond 0.05644 ( 1212) hydrogen bonds : angle 5.57282 ( 3288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 431 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7865 (tp30) cc_final: 0.7572 (tm-30) REVERT: A 129 ASN cc_start: 0.8210 (t0) cc_final: 0.7878 (t0) REVERT: A 220 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8096 (t) REVERT: A 254 TYR cc_start: 0.7707 (p90) cc_final: 0.7443 (p90) REVERT: A 297 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7236 (mm-30) REVERT: A 335 GLU cc_start: 0.8805 (tt0) cc_final: 0.8489 (tm-30) REVERT: A 359 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: A 547 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8952 (mp) REVERT: A 756 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7525 (mtp180) REVERT: A 774 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7642 (tttt) REVERT: A 970 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: B 41 GLU cc_start: 0.7834 (tp30) cc_final: 0.7501 (tm-30) REVERT: B 129 ASN cc_start: 0.8203 (t0) cc_final: 0.7873 (t0) REVERT: B 220 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8062 (t) REVERT: B 254 TYR cc_start: 0.7698 (p90) cc_final: 0.7407 (p90) REVERT: B 297 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7241 (mm-30) REVERT: B 335 GLU cc_start: 0.8774 (tt0) cc_final: 0.8497 (tm-30) REVERT: B 359 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: B 547 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8957 (mp) REVERT: B 756 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7431 (mtp180) REVERT: B 970 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: C 41 GLU cc_start: 0.7847 (tp30) cc_final: 0.7525 (tm-30) REVERT: C 50 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7654 (mm110) REVERT: C 129 ASN cc_start: 0.8173 (t0) cc_final: 0.7866 (t0) REVERT: C 212 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7088 (t0) REVERT: C 254 TYR cc_start: 0.7708 (p90) cc_final: 0.7446 (p90) REVERT: C 335 GLU cc_start: 0.8762 (tt0) cc_final: 0.8480 (tm-30) REVERT: C 370 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7303 (tp30) REVERT: C 547 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8907 (mp) REVERT: C 769 MET cc_start: 0.7879 (ttt) cc_final: 0.7337 (tmt) REVERT: C 774 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7659 (tttt) REVERT: C 970 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: D 41 GLU cc_start: 0.7864 (tp30) cc_final: 0.7531 (tm-30) REVERT: D 50 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7633 (mm110) REVERT: D 129 ASN cc_start: 0.8211 (t0) cc_final: 0.7863 (t0) REVERT: D 220 THR cc_start: 0.8370 (p) cc_final: 0.8087 (t) REVERT: D 335 GLU cc_start: 0.8774 (tt0) cc_final: 0.8497 (tm-30) REVERT: D 359 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: D 369 ASP cc_start: 0.8134 (p0) cc_final: 0.7833 (p0) REVERT: D 547 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8907 (mp) REVERT: D 751 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7455 (mp0) REVERT: D 769 MET cc_start: 0.7853 (ttt) cc_final: 0.7399 (tmt) REVERT: D 774 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7761 (mtpp) REVERT: D 970 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7193 (mp0) outliers start: 78 outliers final: 27 residues processed: 482 average time/residue: 0.9087 time to fit residues: 507.1146 Evaluate side-chains 471 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 429 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 970 GLU Chi-restraints excluded: chain B residue 1001 SER Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 647 HIS Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 1001 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 647 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 924 SER Chi-restraints excluded: chain D residue 970 GLU Chi-restraints excluded: chain D residue 1001 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 65 optimal weight: 9.9990 chunk 234 optimal weight: 1.9990 chunk 338 optimal weight: 9.9990 chunk 353 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 584 ASN A 605 ASN B 584 ASN B 605 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 ASN C 762 GLN C 959 ASN D 584 ASN D 605 ASN D 762 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.146082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122426 restraints weight = 29668.252| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.11 r_work: 0.3249 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33860 Z= 0.128 Angle : 0.570 10.430 46200 Z= 0.300 Chirality : 0.044 0.169 4832 Planarity : 0.004 0.031 6100 Dihedral : 5.321 54.156 4484 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.26 % Rotamer: Outliers : 1.48 % Allowed : 11.90 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.26 (0.13), residues: 4088 helix: 0.38 (0.21), residues: 564 sheet: 0.82 (0.14), residues: 1276 loop : -0.20 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 858 TYR 0.017 0.001 TYR D 101 PHE 0.008 0.001 PHE C 748 TRP 0.041 0.002 TRP D 554 HIS 0.005 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00272 (33856) covalent geometry : angle 0.56644 (46192) SS BOND : bond 0.00756 ( 4) SS BOND : angle 5.11340 ( 8) hydrogen bonds : bond 0.04155 ( 1212) hydrogen bonds : angle 5.21528 ( 3288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 475 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7868 (tp30) cc_final: 0.7537 (tm-30) REVERT: A 76 GLU cc_start: 0.7185 (pp20) cc_final: 0.6950 (pp20) REVERT: A 129 ASN cc_start: 0.8108 (t0) cc_final: 0.7767 (t0) REVERT: A 220 THR cc_start: 0.8323 (p) cc_final: 0.8013 (t) REVERT: A 297 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6996 (mm-30) REVERT: A 756 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7375 (mtp180) REVERT: A 774 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7713 (tptp) REVERT: A 970 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: B 41 GLU cc_start: 0.7839 (tp30) cc_final: 0.7451 (tm-30) REVERT: B 129 ASN cc_start: 0.8118 (t0) cc_final: 0.7769 (t0) REVERT: B 220 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7995 (t) REVERT: B 297 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7006 (mm-30) REVERT: B 335 GLU cc_start: 0.8745 (tt0) cc_final: 0.8472 (tm-30) REVERT: B 359 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: B 769 MET cc_start: 0.7836 (ttt) cc_final: 0.7288 (tmt) REVERT: B 970 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: C 41 GLU cc_start: 0.7791 (tp30) cc_final: 0.7482 (tm-30) REVERT: C 50 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7533 (mm110) REVERT: C 129 ASN cc_start: 0.8082 (t0) cc_final: 0.7787 (t0) REVERT: C 212 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7066 (t0) REVERT: C 252 ARG cc_start: 0.7255 (mmt180) cc_final: 0.7021 (mmm160) REVERT: C 254 TYR cc_start: 0.7699 (p90) cc_final: 0.7417 (p90) REVERT: C 335 GLU cc_start: 0.8733 (tt0) cc_final: 0.8453 (tm-30) REVERT: C 370 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: C 647 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.7383 (m-70) REVERT: C 769 MET cc_start: 0.7803 (ttt) cc_final: 0.7294 (tmt) REVERT: C 774 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7636 (tttt) REVERT: C 970 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: D 41 GLU cc_start: 0.7816 (tp30) cc_final: 0.7442 (tm-30) REVERT: D 50 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7560 (mm110) REVERT: D 129 ASN cc_start: 0.8119 (t0) cc_final: 0.7774 (t0) REVERT: D 220 THR cc_start: 0.8344 (p) cc_final: 0.8034 (t) REVERT: D 335 GLU cc_start: 0.8747 (tt0) cc_final: 0.8460 (tm-30) REVERT: D 369 ASP cc_start: 0.8035 (p0) cc_final: 0.7772 (p0) REVERT: D 751 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7433 (mp0) REVERT: D 769 MET cc_start: 0.7753 (ttt) cc_final: 0.7300 (tmt) REVERT: D 774 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7639 (tttt) REVERT: D 970 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7138 (mp0) outliers start: 52 outliers final: 25 residues processed: 513 average time/residue: 0.8880 time to fit residues: 529.2671 Evaluate side-chains 474 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 440 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 970 GLU Chi-restraints excluded: chain B residue 1001 SER Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 647 HIS Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 1001 SER Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 605 ASN Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 647 HIS Chi-restraints excluded: chain D residue 970 GLU Chi-restraints excluded: chain D residue 1001 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 244 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 393 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 392 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 302 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 805 ASN A 825 GLN B 584 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 959 ASN C 986 ASN D 584 ASN D 762 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.142637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118142 restraints weight = 29507.129| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.11 r_work: 0.3193 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 33860 Z= 0.240 Angle : 0.699 16.796 46200 Z= 0.370 Chirality : 0.048 0.180 4832 Planarity : 0.005 0.037 6100 Dihedral : 5.728 50.019 4484 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.71 % Allowed : 12.19 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.16 (0.13), residues: 4088 helix: 0.08 (0.21), residues: 568 sheet: 0.71 (0.14), residues: 1352 loop : -0.21 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 293 TYR 0.022 0.002 TYR C 101 PHE 0.012 0.002 PHE C 275 TRP 0.039 0.002 TRP A 554 HIS 0.008 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00524 (33856) covalent geometry : angle 0.68915 (46192) SS BOND : bond 0.01613 ( 4) SS BOND : angle 8.96452 ( 8) hydrogen bonds : bond 0.05370 ( 1212) hydrogen bonds : angle 5.45023 ( 3288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 428 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7876 (tp30) cc_final: 0.7548 (tm-30) REVERT: A 129 ASN cc_start: 0.8172 (t0) cc_final: 0.7833 (t0) REVERT: A 220 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8063 (t) REVERT: A 297 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7149 (mm-30) REVERT: A 335 GLU cc_start: 0.8760 (tt0) cc_final: 0.8473 (tm-30) REVERT: A 359 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: A 547 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8934 (mp) REVERT: A 756 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7464 (mtp180) REVERT: A 970 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: B 41 GLU cc_start: 0.7858 (tp30) cc_final: 0.7521 (tm-30) REVERT: B 76 GLU cc_start: 0.7321 (pp20) cc_final: 0.7029 (pp20) REVERT: B 129 ASN cc_start: 0.8171 (t0) cc_final: 0.7838 (t0) REVERT: B 220 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8044 (t) REVERT: B 297 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7165 (mm-30) REVERT: B 335 GLU cc_start: 0.8764 (tt0) cc_final: 0.8485 (tm-30) REVERT: B 359 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: B 547 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8926 (mp) REVERT: B 970 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: C 41 GLU cc_start: 0.7823 (tp30) cc_final: 0.7500 (tm-30) REVERT: C 50 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7625 (mm110) REVERT: C 76 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7517 (pt0) REVERT: C 129 ASN cc_start: 0.8156 (t0) cc_final: 0.7835 (t0) REVERT: C 212 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7075 (t0) REVERT: C 335 GLU cc_start: 0.8741 (tt0) cc_final: 0.8469 (tm-30) REVERT: C 370 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: C 547 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8906 (mp) REVERT: C 769 MET cc_start: 0.7842 (ttt) cc_final: 0.7401 (tmt) REVERT: C 774 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7667 (tttt) REVERT: C 970 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: D 41 GLU cc_start: 0.7856 (tp30) cc_final: 0.7514 (tm-30) REVERT: D 50 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7627 (mm110) REVERT: D 129 ASN cc_start: 0.8183 (t0) cc_final: 0.7827 (t0) REVERT: D 220 THR cc_start: 0.8370 (p) cc_final: 0.8073 (t) REVERT: D 335 GLU cc_start: 0.8753 (tt0) cc_final: 0.8475 (tm-30) REVERT: D 359 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: D 369 ASP cc_start: 0.8106 (p0) cc_final: 0.7833 (p0) REVERT: D 547 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8918 (mp) REVERT: D 751 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7469 (mp0) REVERT: D 769 MET cc_start: 0.7846 (ttt) cc_final: 0.7399 (tmt) REVERT: D 774 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7747 (mtpp) REVERT: D 970 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7192 (mp0) outliers start: 60 outliers final: 26 residues processed: 470 average time/residue: 0.8986 time to fit residues: 490.2072 Evaluate side-chains 465 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 424 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 647 HIS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 970 GLU Chi-restraints excluded: chain B residue 1001 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 1001 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 647 HIS Chi-restraints excluded: chain D residue 970 GLU Chi-restraints excluded: chain D residue 1001 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 165 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 274 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 321 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 762 GLN A 825 GLN B 584 ASN B 726 ASN B 762 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 959 ASN D 584 ASN D 762 GLN D 825 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120824 restraints weight = 29529.897| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.12 r_work: 0.3242 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33860 Z= 0.147 Angle : 0.620 19.636 46200 Z= 0.325 Chirality : 0.045 0.173 4832 Planarity : 0.004 0.045 6100 Dihedral : 5.444 45.586 4484 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.20 % Allowed : 12.50 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.19 (0.13), residues: 4088 helix: 0.17 (0.21), residues: 584 sheet: 0.80 (0.14), residues: 1300 loop : -0.23 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 293 TYR 0.018 0.002 TYR D 101 PHE 0.008 0.001 PHE C 275 TRP 0.041 0.002 TRP A 554 HIS 0.006 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00317 (33856) covalent geometry : angle 0.61206 (46192) SS BOND : bond 0.01175 ( 4) SS BOND : angle 7.41647 ( 8) hydrogen bonds : bond 0.04392 ( 1212) hydrogen bonds : angle 5.25408 ( 3288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 446 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7881 (tp30) cc_final: 0.7505 (tm-30) REVERT: A 76 GLU cc_start: 0.7535 (pm20) cc_final: 0.7286 (pm20) REVERT: A 129 ASN cc_start: 0.8091 (t0) cc_final: 0.7752 (t0) REVERT: A 220 THR cc_start: 0.8327 (p) cc_final: 0.8006 (t) REVERT: A 247 MET cc_start: 0.8267 (ppp) cc_final: 0.7931 (ppp) REVERT: A 254 TYR cc_start: 0.7786 (p90) cc_final: 0.7542 (p90) REVERT: A 297 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7043 (mm-30) REVERT: A 335 GLU cc_start: 0.8728 (tt0) cc_final: 0.8448 (tm-30) REVERT: A 547 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8913 (mp) REVERT: A 769 MET cc_start: 0.7792 (ttt) cc_final: 0.7353 (tmt) REVERT: A 774 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7741 (tptp) REVERT: A 970 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: B 41 GLU cc_start: 0.7826 (tp30) cc_final: 0.7453 (tm-30) REVERT: B 129 ASN cc_start: 0.8079 (t0) cc_final: 0.7718 (t0) REVERT: B 220 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8005 (t) REVERT: B 297 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7077 (mm-30) REVERT: B 335 GLU cc_start: 0.8730 (tt0) cc_final: 0.8463 (tm-30) REVERT: B 359 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: B 547 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8897 (mp) REVERT: B 769 MET cc_start: 0.7790 (ttt) cc_final: 0.7263 (tmt) REVERT: B 970 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: C 41 GLU cc_start: 0.7794 (tp30) cc_final: 0.7481 (tm-30) REVERT: C 50 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7607 (mm110) REVERT: C 76 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7524 (pt0) REVERT: C 129 ASN cc_start: 0.8066 (t0) cc_final: 0.7754 (t0) REVERT: C 212 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7012 (t0) REVERT: C 252 ARG cc_start: 0.7235 (mmt180) cc_final: 0.6998 (mmm160) REVERT: C 254 TYR cc_start: 0.7713 (p90) cc_final: 0.7463 (p90) REVERT: C 335 GLU cc_start: 0.8715 (tt0) cc_final: 0.8446 (tm-30) REVERT: C 769 MET cc_start: 0.7764 (ttt) cc_final: 0.7290 (tmt) REVERT: C 774 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7640 (tttt) REVERT: C 970 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: D 41 GLU cc_start: 0.7804 (tp30) cc_final: 0.7427 (tm-30) REVERT: D 50 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7547 (mm110) REVERT: D 129 ASN cc_start: 0.8121 (t0) cc_final: 0.7775 (t0) REVERT: D 220 THR cc_start: 0.8335 (p) cc_final: 0.8026 (t) REVERT: D 247 MET cc_start: 0.8366 (ppp) cc_final: 0.7958 (ppp) REVERT: D 335 GLU cc_start: 0.8730 (tt0) cc_final: 0.8460 (tm-30) REVERT: D 369 ASP cc_start: 0.8013 (p0) cc_final: 0.7778 (p0) REVERT: D 751 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7444 (mp0) REVERT: D 769 MET cc_start: 0.7774 (ttt) cc_final: 0.7320 (tmt) REVERT: D 774 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7661 (tttt) REVERT: D 825 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: D 970 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7121 (mp0) outliers start: 42 outliers final: 31 residues processed: 475 average time/residue: 0.8651 time to fit residues: 477.8172 Evaluate side-chains 482 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 441 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 647 HIS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 970 GLU Chi-restraints excluded: chain B residue 1001 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 647 HIS Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 1001 SER Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 647 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 825 GLN Chi-restraints excluded: chain D residue 970 GLU Chi-restraints excluded: chain D residue 1001 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 218 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 194 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 329 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 762 GLN A 825 GLN A 978 HIS B 584 ASN B 726 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN C 762 GLN C 959 ASN D 584 ASN D 762 GLN D 825 GLN D 978 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118848 restraints weight = 29688.510| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.10 r_work: 0.3195 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 33860 Z= 0.218 Angle : 0.693 22.449 46200 Z= 0.364 Chirality : 0.047 0.179 4832 Planarity : 0.005 0.041 6100 Dihedral : 5.642 41.792 4484 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.34 % Allowed : 12.59 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.17 (0.13), residues: 4088 helix: 0.08 (0.21), residues: 568 sheet: 0.72 (0.14), residues: 1332 loop : -0.19 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 293 TYR 0.021 0.002 TYR D 101 PHE 0.011 0.002 PHE C 275 TRP 0.038 0.002 TRP A 554 HIS 0.007 0.001 HIS D 978 Details of bonding type rmsd covalent geometry : bond 0.00471 (33856) covalent geometry : angle 0.68387 (46192) SS BOND : bond 0.01761 ( 4) SS BOND : angle 8.33464 ( 8) hydrogen bonds : bond 0.05156 ( 1212) hydrogen bonds : angle 5.39496 ( 3288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8176 Ramachandran restraints generated. 4088 Oldfield, 0 Emsley, 4088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 431 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7923 (tp30) cc_final: 0.7534 (tm-30) REVERT: A 76 GLU cc_start: 0.7675 (pm20) cc_final: 0.7421 (pm20) REVERT: A 129 ASN cc_start: 0.8147 (t0) cc_final: 0.7816 (t0) REVERT: A 220 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8039 (t) REVERT: A 247 MET cc_start: 0.8363 (ppp) cc_final: 0.7999 (ppp) REVERT: A 297 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 335 GLU cc_start: 0.8793 (tt0) cc_final: 0.8498 (tm-30) REVERT: A 359 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: A 547 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8907 (mp) REVERT: A 774 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7668 (tttt) REVERT: A 970 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: B 41 GLU cc_start: 0.7855 (tp30) cc_final: 0.7500 (tm-30) REVERT: B 76 GLU cc_start: 0.7696 (pm20) cc_final: 0.7479 (pm20) REVERT: B 129 ASN cc_start: 0.8143 (t0) cc_final: 0.7817 (t0) REVERT: B 220 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8041 (t) REVERT: B 297 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7155 (mm-30) REVERT: B 335 GLU cc_start: 0.8781 (tt0) cc_final: 0.8495 (tm-30) REVERT: B 359 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: B 547 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8900 (mp) REVERT: B 970 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: C 41 GLU cc_start: 0.7834 (tp30) cc_final: 0.7503 (tm-30) REVERT: C 50 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7625 (mm110) REVERT: C 129 ASN cc_start: 0.8140 (t0) cc_final: 0.7827 (t0) REVERT: C 212 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7089 (t0) REVERT: C 254 TYR cc_start: 0.7714 (p90) cc_final: 0.7472 (p90) REVERT: C 335 GLU cc_start: 0.8750 (tt0) cc_final: 0.8473 (tm-30) REVERT: C 547 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8896 (mp) REVERT: C 769 MET cc_start: 0.7831 (ttt) cc_final: 0.7391 (tmt) REVERT: C 774 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7672 (tttt) REVERT: C 970 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: D 41 GLU cc_start: 0.7842 (tp30) cc_final: 0.7477 (tm-30) REVERT: D 50 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7625 (mm110) REVERT: D 76 GLU cc_start: 0.7258 (pp20) cc_final: 0.7022 (pp20) REVERT: D 129 ASN cc_start: 0.8184 (t0) cc_final: 0.7827 (t0) REVERT: D 220 THR cc_start: 0.8357 (p) cc_final: 0.8055 (t) REVERT: D 247 MET cc_start: 0.8435 (ppp) cc_final: 0.8038 (ppp) REVERT: D 335 GLU cc_start: 0.8770 (tt0) cc_final: 0.8489 (tm-30) REVERT: D 359 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: D 369 ASP cc_start: 0.8066 (p0) cc_final: 0.7818 (p0) REVERT: D 547 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8946 (mp) REVERT: D 769 MET cc_start: 0.7850 (ttt) cc_final: 0.7405 (tmt) REVERT: D 774 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7750 (mtpp) REVERT: D 825 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: D 970 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7189 (mp0) outliers start: 47 outliers final: 30 residues processed: 465 average time/residue: 0.8724 time to fit residues: 471.7971 Evaluate side-chains 475 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 430 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 970 GLU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 647 HIS Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 970 GLU Chi-restraints excluded: chain B residue 1001 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 647 HIS Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 970 GLU Chi-restraints excluded: chain C residue 1001 SER Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 647 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 825 GLN Chi-restraints excluded: chain D residue 970 GLU Chi-restraints excluded: chain D residue 1001 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 138 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 350 optimal weight: 7.9990 chunk 335 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 chunk 314 optimal weight: 0.0030 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 825 GLN B 584 ASN B 726 ASN B 762 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 959 ASN D 584 ASN D 762 GLN D 825 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120173 restraints weight = 29736.299| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.12 r_work: 0.3229 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33860 Z= 0.163 Angle : 0.639 19.647 46200 Z= 0.335 Chirality : 0.046 0.175 4832 Planarity : 0.004 0.035 6100 Dihedral : 5.471 38.387 4484 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.37 % Allowed : 12.59 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.17 (0.13), residues: 4088 helix: 0.11 (0.21), residues: 584 sheet: 0.72 (0.14), residues: 1332 loop : -0.20 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 293 TYR 0.019 0.002 TYR D 101 PHE 0.009 0.001 PHE C 275 TRP 0.040 0.002 TRP A 554 HIS 0.007 0.001 HIS C 978 Details of bonding type rmsd covalent geometry : bond 0.00352 (33856) covalent geometry : angle 0.63092 (46192) SS BOND : bond 0.01294 ( 4) SS BOND : angle 7.52170 ( 8) hydrogen bonds : bond 0.04585 ( 1212) hydrogen bonds : angle 5.29021 ( 3288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16509.11 seconds wall clock time: 280 minutes 38.93 seconds (16838.93 seconds total)