Starting phenix.real_space_refine on Fri May 30 12:10:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3w_38902/05_2025/8y3w_38902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3w_38902/05_2025/8y3w_38902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3w_38902/05_2025/8y3w_38902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3w_38902/05_2025/8y3w_38902.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3w_38902/05_2025/8y3w_38902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3w_38902/05_2025/8y3w_38902.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.035 sd= 0.086 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 130 5.16 5 C 21754 2.51 5 N 5410 2.21 5 O 6292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33586 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7968 Classifications: {'peptide': 957} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 937} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 7996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7996 Classifications: {'peptide': 958} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 938} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 829 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7968 Classifications: {'peptide': 957} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 937} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 7996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7996 Classifications: {'peptide': 958} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 938} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 829 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 19.92, per 1000 atoms: 0.59 Number of scatterers: 33586 At special positions: 0 Unit cell: (103.421, 131.431, 272.557, 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 130 16.00 O 6292 8.00 N 5410 7.00 C 21754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.03 Conformation dependent library (CDL) restraints added in 4.1 seconds 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7712 Finding SS restraints... Secondary structure from input PDB file: 219 helices and 13 sheets defined 63.1% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.724A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.986A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.969A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.795A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.823A pdb=" N ASP A 189 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.781A pdb=" N ASN A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 197' Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.622A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 removed outlier: 4.043A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.804A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.579A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 461 removed outlier: 4.013A pdb=" N SER A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 491 Processing helix chain 'A' and resid 510 through 519 removed outlier: 3.874A pdb=" N GLU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.931A pdb=" N ASP A 526 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE A 528 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 removed outlier: 3.793A pdb=" N LYS A 537 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 removed outlier: 3.635A pdb=" N GLU A 543 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 579 through 598 removed outlier: 4.247A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.681A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.728A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.645A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 669 Processing helix chain 'A' and resid 672 through 676 removed outlier: 3.695A pdb=" N LYS A 675 " --> pdb=" O SER A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 723 Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 752 through 765 removed outlier: 4.416A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 785 removed outlier: 3.589A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.782A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.896A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 856 removed outlier: 3.515A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.820A pdb=" N ASP A 875 " --> pdb=" O GLY A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 895 removed outlier: 3.710A pdb=" N GLU A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 922 removed outlier: 3.627A pdb=" N THR A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 removed outlier: 3.505A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 976 through 991 removed outlier: 4.308A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 991 " --> pdb=" O ARG A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.783A pdb=" N LYS B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.724A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.987A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 108 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.968A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.795A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.822A pdb=" N ASP B 189 " --> pdb=" O LYS B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.781A pdb=" N ASN B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 197' Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 222 through 235 Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.622A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 4.043A pdb=" N ASP B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 321 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.805A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.580A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 461 removed outlier: 4.013A pdb=" N SER B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 492 removed outlier: 3.502A pdb=" N PHE B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 519 removed outlier: 3.875A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.931A pdb=" N ASP B 526 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N PHE B 528 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.794A pdb=" N LYS B 537 " --> pdb=" O GLU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 547 removed outlier: 3.636A pdb=" N GLU B 543 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 546 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 563 Processing helix chain 'B' and resid 579 through 598 removed outlier: 4.248A pdb=" N VAL B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.681A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.728A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.644A pdb=" N PHE B 659 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 669 Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.694A pdb=" N LYS B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 Processing helix chain 'B' and resid 705 through 723 Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 752 through 765 removed outlier: 4.415A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 785 removed outlier: 3.590A pdb=" N ILE B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.782A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'B' and resid 831 through 841 removed outlier: 3.897A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 856 removed outlier: 3.515A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.821A pdb=" N ASP B 875 " --> pdb=" O GLY B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 895 removed outlier: 3.712A pdb=" N GLU B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 922 Processing helix chain 'B' and resid 928 through 934 removed outlier: 3.505A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 963 through 971 Processing helix chain 'B' and resid 976 through 991 removed outlier: 4.308A pdb=" N GLU B 982 " --> pdb=" O HIS B 978 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER B 991 " --> pdb=" O ARG B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1003 Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.724A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.986A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 108 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.969A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 155 through 160 removed outlier: 3.794A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.822A pdb=" N ASP D 189 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.781A pdb=" N ASN D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR D 197 " --> pdb=" O TYR D 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 192 through 197' Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 282 through 298 removed outlier: 3.622A pdb=" N SER D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 4.043A pdb=" N ASP D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 313 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 321 Processing helix chain 'D' and resid 328 through 334 removed outlier: 3.804A pdb=" N HIS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 366 through 372 removed outlier: 3.579A pdb=" N ARG D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 391 Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 447 through 461 removed outlier: 4.013A pdb=" N SER D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 491 Processing helix chain 'D' and resid 510 through 519 removed outlier: 3.875A pdb=" N GLU D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 531 removed outlier: 3.931A pdb=" N ASP D 526 " --> pdb=" O ASN D 523 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE D 528 " --> pdb=" O ASP D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 537 removed outlier: 3.794A pdb=" N LYS D 537 " --> pdb=" O GLU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 547 removed outlier: 3.636A pdb=" N GLU D 543 " --> pdb=" O LYS D 540 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 546 " --> pdb=" O GLU D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 563 Processing helix chain 'D' and resid 567 through 572 Processing helix chain 'D' and resid 579 through 598 removed outlier: 4.248A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.681A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 628 removed outlier: 3.728A pdb=" N HIS D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR D 628 " --> pdb=" O GLU D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 removed outlier: 3.644A pdb=" N PHE D 659 " --> pdb=" O ILE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 669 Processing helix chain 'D' and resid 672 through 676 removed outlier: 3.696A pdb=" N LYS D 675 " --> pdb=" O SER D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 699 Processing helix chain 'D' and resid 705 through 723 Processing helix chain 'D' and resid 729 through 742 Processing helix chain 'D' and resid 752 through 765 removed outlier: 4.416A pdb=" N CYS D 764 " --> pdb=" O ARG D 760 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 785 removed outlier: 3.590A pdb=" N ILE D 772 " --> pdb=" O PRO D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.782A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 826 Processing helix chain 'D' and resid 831 through 841 removed outlier: 3.897A pdb=" N LEU D 841 " --> pdb=" O PHE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 856 removed outlier: 3.515A pdb=" N PHE D 856 " --> pdb=" O HIS D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 876 removed outlier: 3.820A pdb=" N ASP D 875 " --> pdb=" O GLY D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 895 removed outlier: 3.711A pdb=" N GLU D 882 " --> pdb=" O THR D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 922 removed outlier: 3.992A pdb=" N PHE D 916 " --> pdb=" O TYR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 934 removed outlier: 3.505A pdb=" N ILE D 934 " --> pdb=" O GLU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 963 through 971 Processing helix chain 'D' and resid 976 through 991 removed outlier: 4.308A pdb=" N GLU D 982 " --> pdb=" O HIS D 978 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER D 991 " --> pdb=" O ARG D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1003 Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 23 through 40 Processing helix chain 'E' and resid 47 through 52 removed outlier: 3.724A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.986A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 95 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 96 through 108 Processing helix chain 'E' and resid 115 through 122 removed outlier: 3.968A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS E 120 " --> pdb=" O PRO E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 155 through 160 removed outlier: 3.794A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.822A pdb=" N ASP E 189 " --> pdb=" O LYS E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 removed outlier: 3.781A pdb=" N ASN E 196 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR E 197 " --> pdb=" O TYR E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 197' Processing helix chain 'E' and resid 197 through 210 Processing helix chain 'E' and resid 222 through 235 Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 282 through 298 removed outlier: 3.622A pdb=" N SER E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 317 removed outlier: 4.043A pdb=" N ASP E 310 " --> pdb=" O ASP E 306 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS E 315 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 321 Processing helix chain 'E' and resid 328 through 334 removed outlier: 3.804A pdb=" N HIS E 332 " --> pdb=" O ILE E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 366 Processing helix chain 'E' and resid 366 through 372 removed outlier: 3.579A pdb=" N ARG E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 391 Processing helix chain 'E' and resid 417 through 426 Processing helix chain 'E' and resid 431 through 445 Processing helix chain 'E' and resid 447 through 461 removed outlier: 4.013A pdb=" N SER E 451 " --> pdb=" O ARG E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 492 Processing helix chain 'E' and resid 510 through 519 removed outlier: 3.874A pdb=" N GLU E 516 " --> pdb=" O LEU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 531 removed outlier: 3.931A pdb=" N ASP E 526 " --> pdb=" O ASN E 523 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE E 528 " --> pdb=" O ASP E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 537 removed outlier: 3.794A pdb=" N LYS E 537 " --> pdb=" O GLU E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 547 removed outlier: 3.636A pdb=" N GLU E 543 " --> pdb=" O LYS E 540 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE E 544 " --> pdb=" O ILE E 541 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER E 546 " --> pdb=" O GLU E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 563 Processing helix chain 'E' and resid 579 through 598 removed outlier: 4.247A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 removed outlier: 3.682A pdb=" N VAL E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 628 removed outlier: 3.728A pdb=" N HIS E 609 " --> pdb=" O PHE E 605 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR E 628 " --> pdb=" O GLU E 624 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 659 removed outlier: 3.645A pdb=" N PHE E 659 " --> pdb=" O ILE E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 669 Processing helix chain 'E' and resid 672 through 676 removed outlier: 3.696A pdb=" N LYS E 675 " --> pdb=" O SER E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 699 Processing helix chain 'E' and resid 705 through 723 Processing helix chain 'E' and resid 729 through 742 Processing helix chain 'E' and resid 752 through 765 removed outlier: 4.415A pdb=" N CYS E 764 " --> pdb=" O ARG E 760 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN E 765 " --> pdb=" O LEU E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 785 removed outlier: 3.590A pdb=" N ILE E 772 " --> pdb=" O PRO E 768 " (cutoff:3.500A) Processing helix chain 'E' and resid 800 through 812 removed outlier: 3.782A pdb=" N TYR E 804 " --> pdb=" O TYR E 800 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 826 Processing helix chain 'E' and resid 831 through 841 removed outlier: 3.897A pdb=" N LEU E 841 " --> pdb=" O PHE E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 856 removed outlier: 3.516A pdb=" N PHE E 856 " --> pdb=" O HIS E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 872 through 876 removed outlier: 3.821A pdb=" N ASP E 875 " --> pdb=" O GLY E 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 878 through 895 removed outlier: 3.712A pdb=" N GLU E 882 " --> pdb=" O THR E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 922 Processing helix chain 'E' and resid 928 through 934 removed outlier: 3.505A pdb=" N ILE E 934 " --> pdb=" O GLU E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 945 Processing helix chain 'E' and resid 963 through 971 Processing helix chain 'E' and resid 976 through 991 removed outlier: 4.308A pdb=" N GLU E 982 " --> pdb=" O HIS E 978 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER E 991 " --> pdb=" O ARG E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1003 Processing helix chain 'F' and resid 95 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 5.802A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 removed outlier: 5.802A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AA5, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.524A pdb=" N VAL C 87 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 5.803A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AA9, first strand: chain 'D' and resid 573 through 575 removed outlier: 4.233A pdb=" N TYR D 574 " --> pdb=" O TYR F 16 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 150 through 152 removed outlier: 5.802A pdb=" N SER E 150 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS E 169 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE E 152 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE E 44 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 339 through 340 Processing sheet with id=AB3, first strand: chain 'F' and resid 27 through 28 removed outlier: 3.523A pdb=" N VAL F 87 " --> pdb=" O GLU F 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 45 through 46 1590 hydrogen bonds defined for protein. 4542 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: 13.86 Time building geometry restraints manager: 9.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10451 1.34 - 1.46: 8519 1.46 - 1.58: 15164 1.58 - 1.70: 0 1.70 - 1.83: 216 Bond restraints: 34350 Sorted by residual: bond pdb=" C ASN B 563 " pdb=" N LYS B 564 " ideal model delta sigma weight residual 1.334 1.294 0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" C ASN A 563 " pdb=" N LYS A 564 " ideal model delta sigma weight residual 1.334 1.295 0.039 1.25e-02 6.40e+03 9.85e+00 bond pdb=" C ASN D 563 " pdb=" N LYS D 564 " ideal model delta sigma weight residual 1.334 1.295 0.039 1.25e-02 6.40e+03 9.83e+00 bond pdb=" C ASN E 563 " pdb=" N LYS E 564 " ideal model delta sigma weight residual 1.334 1.295 0.039 1.25e-02 6.40e+03 9.67e+00 bond pdb=" C SER B 317 " pdb=" N PRO B 318 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.38e-02 5.25e+03 8.16e+00 ... (remaining 34345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 44470 2.55 - 5.10: 1564 5.10 - 7.65: 201 7.65 - 10.20: 37 10.20 - 12.74: 10 Bond angle restraints: 46282 Sorted by residual: angle pdb=" N VAL D 565 " pdb=" CA VAL D 565 " pdb=" C VAL D 565 " ideal model delta sigma weight residual 112.83 101.23 11.60 9.90e-01 1.02e+00 1.37e+02 angle pdb=" N VAL A 565 " pdb=" CA VAL A 565 " pdb=" C VAL A 565 " ideal model delta sigma weight residual 113.22 101.23 11.99 1.23e+00 6.61e-01 9.51e+01 angle pdb=" C ILE E 631 " pdb=" N ASP E 632 " pdb=" CA ASP E 632 " ideal model delta sigma weight residual 122.60 111.16 11.44 1.56e+00 4.11e-01 5.38e+01 angle pdb=" CA TYR E 11 " pdb=" CB TYR E 11 " pdb=" CG TYR E 11 " ideal model delta sigma weight residual 113.90 126.14 -12.24 1.80e+00 3.09e-01 4.62e+01 angle pdb=" C ARG E 10 " pdb=" N TYR E 11 " pdb=" CA TYR E 11 " ideal model delta sigma weight residual 121.54 134.28 -12.74 1.91e+00 2.74e-01 4.45e+01 ... (remaining 46277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 18920 15.84 - 31.68: 1169 31.68 - 47.52: 308 47.52 - 63.36: 49 63.36 - 79.20: 28 Dihedral angle restraints: 20474 sinusoidal: 8496 harmonic: 11978 Sorted by residual: dihedral pdb=" CA SER A 957 " pdb=" C SER A 957 " pdb=" N TRP A 958 " pdb=" CA TRP A 958 " ideal model delta harmonic sigma weight residual 180.00 115.08 64.92 0 5.00e+00 4.00e-02 1.69e+02 dihedral pdb=" CA SER E 957 " pdb=" C SER E 957 " pdb=" N TRP E 958 " pdb=" CA TRP E 958 " ideal model delta harmonic sigma weight residual 180.00 115.09 64.91 0 5.00e+00 4.00e-02 1.69e+02 dihedral pdb=" CA SER D 957 " pdb=" C SER D 957 " pdb=" N TRP D 958 " pdb=" CA TRP D 958 " ideal model delta harmonic sigma weight residual 180.00 115.11 64.89 0 5.00e+00 4.00e-02 1.68e+02 ... (remaining 20471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4336 0.081 - 0.161: 548 0.161 - 0.242: 55 0.242 - 0.322: 3 0.322 - 0.403: 2 Chirality restraints: 4944 Sorted by residual: chirality pdb=" CB VAL F 95 " pdb=" CA VAL F 95 " pdb=" CG1 VAL F 95 " pdb=" CG2 VAL F 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CB VAL C 95 " pdb=" CA VAL C 95 " pdb=" CG1 VAL C 95 " pdb=" CG2 VAL C 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA LYS E 564 " pdb=" N LYS E 564 " pdb=" C LYS E 564 " pdb=" CB LYS E 564 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 4941 not shown) Planarity restraints: 5890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 866 " -0.032 2.00e-02 2.50e+03 6.33e-02 4.01e+01 pdb=" C MET A 866 " 0.110 2.00e-02 2.50e+03 pdb=" O MET A 866 " -0.040 2.00e-02 2.50e+03 pdb=" N ASN A 867 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 866 " 0.032 2.00e-02 2.50e+03 6.33e-02 4.01e+01 pdb=" C MET D 866 " -0.110 2.00e-02 2.50e+03 pdb=" O MET D 866 " 0.040 2.00e-02 2.50e+03 pdb=" N ASN D 867 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 866 " -0.032 2.00e-02 2.50e+03 6.32e-02 4.00e+01 pdb=" C MET E 866 " 0.109 2.00e-02 2.50e+03 pdb=" O MET E 866 " -0.040 2.00e-02 2.50e+03 pdb=" N ASN E 867 " -0.037 2.00e-02 2.50e+03 ... (remaining 5887 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1321 2.70 - 3.25: 33446 3.25 - 3.80: 53673 3.80 - 4.35: 70749 4.35 - 4.90: 113917 Nonbonded interactions: 273106 Sorted by model distance: nonbonded pdb=" OH TYR E 11 " pdb=" OD2 ASP E 291 " model vdw 2.146 3.040 nonbonded pdb=" OG SER D 570 " pdb=" OH TYR D 625 " model vdw 2.200 3.040 nonbonded pdb=" O GLU B 624 " pdb=" OG1 THR B 628 " model vdw 2.225 3.040 nonbonded pdb=" O GLU D 624 " pdb=" OG1 THR D 628 " model vdw 2.225 3.040 nonbonded pdb=" O GLU E 624 " pdb=" OG1 THR E 628 " model vdw 2.226 3.040 ... (remaining 273101 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: 0.16 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 376 or (resid 377 and (name N or name CA or nam \ e C or name O or name CB )) or resid 378 through 565 or resid 577 through 898 or \ resid 912 through 1005)) selection = (chain 'B' and (resid 12 through 491 or resid 506 through 628 or (resid 629 and \ (name N or name CA or name C or name O or name CB )) or resid 630 through 631 or \ resid 644 through 986 or (resid 987 and (name N or name CA or name C or name O \ or name CB )) or resid 988 through 1005)) selection = (chain 'D' and (resid 12 through 376 or (resid 377 and (name N or name CA or nam \ e C or name O or name CB )) or resid 378 through 565 or resid 577 through 898 or \ resid 912 through 1005)) selection = (chain 'E' and (resid 12 through 491 or resid 506 through 628 or (resid 629 and \ (name N or name CA or name C or name O or name CB )) or resid 630 through 631 or \ resid 644 through 986 or (resid 987 and (name N or name CA or name C or name O \ or name CB )) or resid 988 through 1005)) } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.350 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 73.880 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 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 : 0.006 0.075 34350 Z= 0.302 Angle : 1.137 12.745 46282 Z= 0.690 Chirality : 0.056 0.403 4944 Planarity : 0.007 0.063 5890 Dihedral : 11.850 79.203 12762 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.44 % Favored : 89.95 % Rotamer: Outliers : 0.49 % Allowed : 4.21 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.97 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.10), residues: 3982 helix: -2.78 (0.08), residues: 2464 sheet: -3.45 (0.43), residues: 88 loop : -3.36 (0.13), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP F 25 HIS 0.016 0.002 HIS B 339 PHE 0.033 0.003 PHE A 839 TYR 0.052 0.003 TYR E 11 ARG 0.009 0.001 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.17030 ( 1590) hydrogen bonds : angle 8.63088 ( 4542) covalent geometry : bond 0.00610 (34350) covalent geometry : angle 1.13717 (46282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 523 time to evaluate : 3.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.4086 (t-100) cc_final: 0.3083 (m-90) REVERT: A 225 ILE cc_start: 0.8019 (mm) cc_final: 0.7751 (mt) REVERT: A 290 MET cc_start: 0.1546 (tpp) cc_final: 0.1070 (mtt) REVERT: A 291 ASP cc_start: 0.4393 (m-30) cc_final: 0.4116 (m-30) REVERT: A 382 ASN cc_start: 0.7363 (m-40) cc_final: 0.6667 (m-40) REVERT: A 661 ILE cc_start: 0.2101 (mp) cc_final: 0.1510 (pt) REVERT: A 676 ILE cc_start: 0.4364 (mm) cc_final: 0.3369 (mm) REVERT: A 757 TRP cc_start: 0.4509 (m-90) cc_final: 0.4069 (t-100) REVERT: A 978 HIS cc_start: 0.8462 (t-90) cc_final: 0.8243 (t-90) REVERT: B 124 MET cc_start: 0.7502 (mmm) cc_final: 0.7204 (mmm) REVERT: B 780 VAL cc_start: 0.8754 (t) cc_final: 0.7977 (m) REVERT: B 845 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5527 (pp) REVERT: C 66 ILE cc_start: 0.7013 (mt) cc_final: 0.6765 (mp) REVERT: C 85 LYS cc_start: 0.7432 (tptp) cc_final: 0.6805 (tmtt) REVERT: D 29 CYS cc_start: 0.1200 (m) cc_final: 0.0562 (m) REVERT: D 84 TYR cc_start: 0.2881 (m-10) cc_final: 0.0878 (m-10) REVERT: D 167 LEU cc_start: 0.5812 (tt) cc_final: 0.5600 (tt) REVERT: D 445 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5899 (pt) REVERT: D 548 ASN cc_start: 0.5386 (p0) cc_final: 0.4966 (m-40) REVERT: E 512 LEU cc_start: 0.8160 (mt) cc_final: 0.7852 (tt) REVERT: E 531 MET cc_start: 0.8389 (mmm) cc_final: 0.8132 (mmt) REVERT: E 839 PHE cc_start: 0.8009 (t80) cc_final: 0.7563 (t80) REVERT: E 920 TYR cc_start: 0.7343 (t80) cc_final: 0.6615 (t80) REVERT: E 936 MET cc_start: 0.2366 (mpt) cc_final: -0.0791 (ptm) outliers start: 18 outliers final: 3 residues processed: 540 average time/residue: 0.5049 time to fit residues: 424.2019 Evaluate side-chains 256 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 251 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 15 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 5.9990 chunk 303 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 204 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 313 optimal weight: 0.0980 chunk 121 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 363 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 67 HIS A 171 HIS A 182 ASN A 226 ASN A 299 ASN A 467 ASN A 483 GLN A 591 ASN A 658 HIS A 698 GLN A 797 ASN A 829 GLN A 832 GLN A 863 ASN A 973 ASN A 992 ASN B 24 ASN B 171 HIS B 182 ASN B 297 GLN B 467 ASN B 521 ASN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN B 829 GLN B 832 GLN B 939 GLN B 973 ASN B 990 ASN C 21 ASN C 88 HIS D 24 ASN D 67 HIS D 171 HIS D 192 ASN D 236 GLN D 297 GLN D 467 ASN D 483 GLN D 658 HIS D 698 GLN D 782 GLN D 797 ASN D 829 GLN D 832 GLN D 990 ASN D 992 ASN E 24 ASN E 297 GLN E 467 ASN E 521 ASN E 529 ASN E 591 ASN E 698 GLN E 829 GLN E 832 GLN E 863 ASN E 973 ASN E 990 ASN F 21 ASN F 88 HIS Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.109698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.096373 restraints weight = 196011.353| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 4.73 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34350 Z= 0.139 Angle : 0.699 12.882 46282 Z= 0.373 Chirality : 0.043 0.258 4944 Planarity : 0.004 0.050 5890 Dihedral : 6.702 57.240 4433 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.76 % Favored : 92.74 % Rotamer: Outliers : 1.94 % Allowed : 8.12 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.12), residues: 3982 helix: -0.98 (0.10), residues: 2384 sheet: -3.48 (0.36), residues: 132 loop : -3.02 (0.14), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 25 HIS 0.008 0.001 HIS D 339 PHE 0.042 0.002 PHE A 839 TYR 0.025 0.002 TYR B 940 ARG 0.009 0.001 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 1590) hydrogen bonds : angle 5.19839 ( 4542) covalent geometry : bond 0.00284 (34350) covalent geometry : angle 0.69942 (46282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 292 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7622 (pt0) REVERT: A 59 TRP cc_start: 0.4939 (t-100) cc_final: 0.3559 (m-90) REVERT: A 68 GLU cc_start: 0.3043 (OUTLIER) cc_final: 0.2079 (tt0) REVERT: A 225 ILE cc_start: 0.8257 (mm) cc_final: 0.8052 (mt) REVERT: A 395 CYS cc_start: 0.6215 (OUTLIER) cc_final: 0.5897 (p) REVERT: A 569 MET cc_start: 0.7128 (tmm) cc_final: 0.6050 (tmm) REVERT: A 601 TRP cc_start: 0.3945 (t-100) cc_final: 0.2946 (t-100) REVERT: A 676 ILE cc_start: 0.4190 (mm) cc_final: 0.3434 (mm) REVERT: A 771 ILE cc_start: 0.8096 (mm) cc_final: 0.7779 (tt) REVERT: A 853 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7334 (tt) REVERT: A 890 GLU cc_start: 0.3891 (OUTLIER) cc_final: 0.3345 (tt0) REVERT: A 978 HIS cc_start: 0.8559 (t-90) cc_final: 0.8297 (t-90) REVERT: B 470 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8270 (p) REVERT: B 791 TYR cc_start: 0.5205 (OUTLIER) cc_final: 0.4427 (m-80) REVERT: B 936 MET cc_start: 0.5654 (mpt) cc_final: 0.3748 (ppp) REVERT: D 84 TYR cc_start: 0.2044 (m-10) cc_final: 0.1499 (m-10) REVERT: D 242 LYS cc_start: 0.7450 (mtpt) cc_final: 0.7250 (mtpt) REVERT: D 259 ILE cc_start: 0.8649 (mt) cc_final: 0.8331 (mm) REVERT: D 548 ASN cc_start: 0.4540 (p0) cc_final: 0.4230 (m110) REVERT: D 696 THR cc_start: 0.6761 (m) cc_final: 0.6547 (p) REVERT: D 936 MET cc_start: 0.2082 (tmm) cc_final: 0.1055 (ptt) REVERT: E 238 ASP cc_start: 0.6151 (t0) cc_final: 0.5948 (t70) REVERT: E 531 MET cc_start: 0.8626 (mmm) cc_final: 0.7984 (mmt) REVERT: E 866 MET cc_start: 0.2484 (ttt) cc_final: 0.2002 (ttt) REVERT: E 936 MET cc_start: 0.1877 (mpt) cc_final: -0.0693 (ptm) REVERT: F 27 VAL cc_start: 0.6354 (OUTLIER) cc_final: 0.5946 (m) outliers start: 72 outliers final: 25 residues processed: 350 average time/residue: 0.4235 time to fit residues: 245.6727 Evaluate side-chains 231 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 83 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 168 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 258 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 329 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 182 ASN A 202 ASN A 591 ASN A 829 GLN ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS B 391 ASN B 591 ASN B 614 ASN B 658 HIS C 17 HIS D 226 ASN D 391 ASN E 391 ASN E 591 ASN E 614 ASN E 658 HIS E 797 ASN ** E 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.105503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.091927 restraints weight = 188849.539| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 4.66 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34350 Z= 0.163 Angle : 0.688 9.767 46282 Z= 0.366 Chirality : 0.044 0.248 4944 Planarity : 0.004 0.045 5890 Dihedral : 6.147 56.502 4428 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.71 % Favored : 91.94 % Rotamer: Outliers : 2.00 % Allowed : 9.98 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3982 helix: -0.28 (0.10), residues: 2374 sheet: -3.41 (0.36), residues: 132 loop : -2.68 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 25 HIS 0.009 0.001 HIS A 979 PHE 0.029 0.002 PHE A 839 TYR 0.022 0.002 TYR A 193 ARG 0.007 0.001 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 1590) hydrogen bonds : angle 4.77428 ( 4542) covalent geometry : bond 0.00351 (34350) covalent geometry : angle 0.68835 (46282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 233 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7563 (pt0) REVERT: A 68 GLU cc_start: 0.3395 (OUTLIER) cc_final: 0.2414 (tt0) REVERT: A 98 MET cc_start: 0.7608 (tpp) cc_final: 0.7133 (pmm) REVERT: A 225 ILE cc_start: 0.8552 (mm) cc_final: 0.8341 (mt) REVERT: A 291 ASP cc_start: 0.5669 (m-30) cc_final: 0.5397 (m-30) REVERT: A 569 MET cc_start: 0.6980 (tmm) cc_final: 0.6102 (tmm) REVERT: A 771 ILE cc_start: 0.8291 (mm) cc_final: 0.7974 (tt) REVERT: A 853 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7472 (tt) REVERT: A 890 GLU cc_start: 0.3804 (OUTLIER) cc_final: 0.3292 (tt0) REVERT: A 936 MET cc_start: 0.1615 (tmm) cc_final: 0.0661 (mpp) REVERT: A 951 TYR cc_start: 0.3423 (OUTLIER) cc_final: 0.1858 (t80) REVERT: A 978 HIS cc_start: 0.8659 (t-90) cc_final: 0.8436 (t-90) REVERT: B 791 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.4734 (m-80) REVERT: B 936 MET cc_start: 0.5942 (mpt) cc_final: 0.3568 (ptt) REVERT: D 936 MET cc_start: 0.2464 (tmm) cc_final: 0.1715 (ptt) REVERT: D 976 MET cc_start: 0.1720 (tpp) cc_final: 0.1474 (tpp) REVERT: E 396 MET cc_start: 0.7420 (mtt) cc_final: 0.7158 (mtt) REVERT: E 531 MET cc_start: 0.8765 (mmm) cc_final: 0.8115 (mmt) REVERT: E 936 MET cc_start: 0.2000 (mpt) cc_final: -0.1264 (ptm) REVERT: E 976 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.4774 (mmp) REVERT: F 73 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6825 (mt) outliers start: 74 outliers final: 33 residues processed: 293 average time/residue: 0.4460 time to fit residues: 220.2723 Evaluate side-chains 224 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 951 TYR Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 976 MET Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 281 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 chunk 10 optimal weight: 0.0370 chunk 249 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 363 optimal weight: 3.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 349 HIS A 391 ASN A 487 GLN A 698 GLN A 881 HIS A 910 ASN A 927 ASN ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 297 GLN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN D 58 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN D 299 ASN D 349 HIS D 529 ASN D 698 GLN D 782 GLN D 829 GLN E 297 GLN ** E 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 698 GLN E 765 ASN E 829 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.098672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.085201 restraints weight = 184583.455| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 4.50 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.7013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 34350 Z= 0.224 Angle : 0.777 14.451 46282 Z= 0.413 Chirality : 0.047 0.228 4944 Planarity : 0.005 0.084 5890 Dihedral : 6.337 59.471 4428 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.02 % Favored : 90.63 % Rotamer: Outliers : 2.37 % Allowed : 11.03 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 3982 helix: -0.23 (0.10), residues: 2374 sheet: -3.37 (0.35), residues: 156 loop : -2.57 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP F 25 HIS 0.016 0.002 HIS A 128 PHE 0.033 0.003 PHE D 45 TYR 0.026 0.003 TYR A 313 ARG 0.008 0.001 ARG D 348 Details of bonding type rmsd hydrogen bonds : bond 0.05097 ( 1590) hydrogen bonds : angle 5.07668 ( 4542) covalent geometry : bond 0.00482 (34350) covalent geometry : angle 0.77672 (46282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 252 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.3680 (OUTLIER) cc_final: 0.2824 (tt0) REVERT: A 98 MET cc_start: 0.7281 (tpp) cc_final: 0.6981 (pmm) REVERT: A 106 ASP cc_start: 0.8199 (t0) cc_final: 0.7987 (m-30) REVERT: A 200 ILE cc_start: 0.6795 (mt) cc_final: 0.6463 (mm) REVERT: A 224 ASN cc_start: 0.4776 (OUTLIER) cc_final: 0.4467 (m-40) REVERT: A 569 MET cc_start: 0.6914 (tmm) cc_final: 0.6363 (tmm) REVERT: A 772 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7381 (tp) REVERT: A 787 ILE cc_start: 0.6786 (tt) cc_final: 0.6458 (pt) REVERT: A 792 SER cc_start: 0.5779 (t) cc_final: 0.5508 (p) REVERT: A 871 ILE cc_start: 0.3238 (OUTLIER) cc_final: 0.2927 (mt) REVERT: A 890 GLU cc_start: 0.4550 (OUTLIER) cc_final: 0.3992 (tt0) REVERT: A 936 MET cc_start: 0.1981 (tmm) cc_final: 0.0729 (mpp) REVERT: A 978 HIS cc_start: 0.8576 (t-90) cc_final: 0.8278 (t-90) REVERT: B 396 MET cc_start: 0.7545 (mtp) cc_final: 0.6948 (mmt) REVERT: B 519 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7105 (mpp) REVERT: C 98 ILE cc_start: 0.8159 (mm) cc_final: 0.7934 (mm) REVERT: D 107 PHE cc_start: 0.4848 (OUTLIER) cc_final: 0.3569 (m-10) REVERT: D 215 PHE cc_start: 0.3526 (OUTLIER) cc_final: 0.3151 (m-80) REVERT: D 216 ILE cc_start: 0.7179 (mt) cc_final: 0.6900 (mm) REVERT: D 385 PHE cc_start: 0.7047 (t80) cc_final: 0.5892 (t80) REVERT: D 839 PHE cc_start: 0.6294 (t80) cc_final: 0.5919 (t80) REVERT: D 866 MET cc_start: 0.6794 (mmp) cc_final: 0.6480 (tpp) REVERT: D 936 MET cc_start: 0.2409 (tmm) cc_final: 0.1811 (ptt) REVERT: D 977 LYS cc_start: 0.5736 (OUTLIER) cc_final: 0.5505 (tptm) REVERT: D 979 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7932 (t-170) REVERT: E 396 MET cc_start: 0.7419 (mtt) cc_final: 0.7076 (mtt) REVERT: E 519 MET cc_start: 0.6839 (mmt) cc_final: 0.6568 (mmt) REVERT: E 531 MET cc_start: 0.8816 (mmm) cc_final: 0.8200 (mmt) REVERT: E 920 TYR cc_start: 0.6135 (t80) cc_final: 0.5861 (t80) REVERT: E 931 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: E 936 MET cc_start: 0.2343 (mpt) cc_final: 0.1131 (mtt) REVERT: E 976 MET cc_start: 0.5642 (mmp) cc_final: 0.5136 (mmp) outliers start: 88 outliers final: 37 residues processed: 322 average time/residue: 0.4173 time to fit residues: 227.0646 Evaluate side-chains 232 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 931 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 346 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 373 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 134 optimal weight: 0.0020 chunk 48 optimal weight: 0.0970 chunk 196 optimal weight: 7.9990 chunk 352 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 333 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 HIS D 992 ASN E 563 ASN E 978 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.100576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.087140 restraints weight = 189680.799| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 4.56 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34350 Z= 0.121 Angle : 0.627 11.726 46282 Z= 0.330 Chirality : 0.042 0.234 4944 Planarity : 0.004 0.049 5890 Dihedral : 5.751 55.660 4428 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.96 % Favored : 92.67 % Rotamer: Outliers : 1.75 % Allowed : 12.70 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3982 helix: 0.25 (0.11), residues: 2382 sheet: -3.23 (0.39), residues: 132 loop : -2.41 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 143 HIS 0.007 0.001 HIS D 128 PHE 0.018 0.001 PHE D 45 TYR 0.031 0.002 TYR A 539 ARG 0.005 0.000 ARG D 566 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 1590) hydrogen bonds : angle 4.46806 ( 4542) covalent geometry : bond 0.00252 (34350) covalent geometry : angle 0.62703 (46282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 199 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.3437 (OUTLIER) cc_final: 0.2590 (tt0) REVERT: A 98 MET cc_start: 0.7595 (tpp) cc_final: 0.7329 (pmm) REVERT: A 225 ILE cc_start: 0.9004 (mm) cc_final: 0.8796 (mp) REVERT: A 569 MET cc_start: 0.7195 (tmm) cc_final: 0.6217 (tmm) REVERT: A 792 SER cc_start: 0.5958 (t) cc_final: 0.5625 (p) REVERT: A 890 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.3942 (tt0) REVERT: A 936 MET cc_start: 0.1821 (tmm) cc_final: 0.0957 (mpp) REVERT: A 978 HIS cc_start: 0.8707 (t-90) cc_final: 0.8463 (t70) REVERT: B 519 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6808 (mpp) REVERT: C 93 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.5392 (tptp) REVERT: D 107 PHE cc_start: 0.5154 (OUTLIER) cc_final: 0.3860 (m-10) REVERT: D 192 ASN cc_start: -0.0549 (OUTLIER) cc_final: -0.0790 (m110) REVERT: D 193 TYR cc_start: 0.0048 (t80) cc_final: -0.0540 (t80) REVERT: D 216 ILE cc_start: 0.6714 (mt) cc_final: 0.6415 (mm) REVERT: D 356 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.7012 (p90) REVERT: D 421 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7041 (ttm) REVERT: D 569 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6572 (ppp) REVERT: D 839 PHE cc_start: 0.6431 (t80) cc_final: 0.6069 (t80) REVERT: D 936 MET cc_start: 0.1846 (tmm) cc_final: 0.1208 (ptt) REVERT: D 979 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7819 (t-170) REVERT: E 531 MET cc_start: 0.8765 (mmm) cc_final: 0.8094 (mmt) REVERT: E 936 MET cc_start: 0.1625 (mpt) cc_final: 0.0816 (mtt) REVERT: E 976 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5187 (mmp) outliers start: 65 outliers final: 29 residues processed: 246 average time/residue: 0.4191 time to fit residues: 174.3946 Evaluate side-chains 218 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 3.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 563 ASN Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 976 MET Chi-restraints excluded: chain F residue 52 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 34 optimal weight: 0.8980 chunk 315 optimal weight: 0.9980 chunk 385 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 116 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 345 optimal weight: 0.8980 chunk 368 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS A 614 ASN A 765 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 HIS ** E 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.101007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.087755 restraints weight = 190173.243| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 4.52 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34350 Z= 0.112 Angle : 0.597 9.758 46282 Z= 0.315 Chirality : 0.041 0.240 4944 Planarity : 0.003 0.049 5890 Dihedral : 5.441 52.508 4428 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.96 % Favored : 92.69 % Rotamer: Outliers : 1.62 % Allowed : 13.54 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 3982 helix: 0.49 (0.11), residues: 2400 sheet: -3.20 (0.33), residues: 180 loop : -2.20 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 25 HIS 0.009 0.001 HIS D 128 PHE 0.026 0.001 PHE E 942 TYR 0.032 0.001 TYR A 539 ARG 0.006 0.000 ARG D 566 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 1590) hydrogen bonds : angle 4.28498 ( 4542) covalent geometry : bond 0.00230 (34350) covalent geometry : angle 0.59673 (46282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 4.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.3342 (OUTLIER) cc_final: 0.2423 (tt0) REVERT: A 98 MET cc_start: 0.7519 (tpp) cc_final: 0.7132 (pmm) REVERT: A 166 TYR cc_start: 0.4359 (m-80) cc_final: 0.3832 (m-80) REVERT: A 204 MET cc_start: 0.6824 (mtt) cc_final: 0.6618 (mtt) REVERT: A 569 MET cc_start: 0.6919 (tmm) cc_final: 0.6126 (tmm) REVERT: A 620 ILE cc_start: 0.5622 (pt) cc_final: 0.5033 (tp) REVERT: A 745 PRO cc_start: 0.6566 (Cg_endo) cc_final: 0.6330 (Cg_exo) REVERT: A 792 SER cc_start: 0.5969 (t) cc_final: 0.5757 (p) REVERT: A 866 MET cc_start: 0.6208 (tpp) cc_final: 0.5912 (tpp) REVERT: A 890 GLU cc_start: 0.4499 (OUTLIER) cc_final: 0.3982 (tt0) REVERT: A 936 MET cc_start: 0.1514 (tmm) cc_final: 0.0850 (mpp) REVERT: A 978 HIS cc_start: 0.8668 (t-90) cc_final: 0.8439 (t70) REVERT: B 124 MET cc_start: 0.7469 (tpp) cc_final: 0.7227 (mmm) REVERT: B 157 ASP cc_start: 0.7215 (m-30) cc_final: 0.6864 (m-30) REVERT: B 519 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6840 (mpp) REVERT: B 552 TYR cc_start: 0.6737 (p90) cc_final: 0.6442 (p90) REVERT: B 791 TYR cc_start: 0.5341 (OUTLIER) cc_final: 0.5062 (m-80) REVERT: C 93 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.5856 (tptp) REVERT: D 107 PHE cc_start: 0.5168 (OUTLIER) cc_final: 0.3917 (m-10) REVERT: D 569 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6304 (ppp) REVERT: D 645 PHE cc_start: 0.4752 (t80) cc_final: 0.4187 (t80) REVERT: D 839 PHE cc_start: 0.6486 (t80) cc_final: 0.6095 (t80) REVERT: D 877 PHE cc_start: -0.0786 (OUTLIER) cc_final: -0.1806 (p90) REVERT: D 979 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7796 (t-170) REVERT: E 706 VAL cc_start: 0.6048 (OUTLIER) cc_final: 0.5765 (p) REVERT: E 870 ARG cc_start: 0.3985 (OUTLIER) cc_final: 0.1208 (ptp90) REVERT: E 936 MET cc_start: 0.1438 (mpt) cc_final: 0.0552 (mtt) outliers start: 60 outliers final: 30 residues processed: 243 average time/residue: 0.4294 time to fit residues: 175.6399 Evaluate side-chains 217 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 706 VAL Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 870 ARG Chi-restraints excluded: chain F residue 52 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 297 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 386 ASN D 765 ASN D 973 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.097449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.084030 restraints weight = 184883.389| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 4.49 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.8188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 34350 Z= 0.161 Angle : 0.650 9.591 46282 Z= 0.343 Chirality : 0.043 0.221 4944 Planarity : 0.004 0.049 5890 Dihedral : 5.554 51.970 4428 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.16 % Favored : 91.51 % Rotamer: Outliers : 1.91 % Allowed : 13.51 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 3982 helix: 0.46 (0.11), residues: 2388 sheet: -3.16 (0.37), residues: 156 loop : -2.22 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 25 HIS 0.014 0.001 HIS A 128 PHE 0.020 0.002 PHE D 528 TYR 0.028 0.002 TYR A 539 ARG 0.005 0.001 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 1590) hydrogen bonds : angle 4.55342 ( 4542) covalent geometry : bond 0.00349 (34350) covalent geometry : angle 0.64958 (46282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 197 time to evaluate : 4.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.3448 (OUTLIER) cc_final: 0.2566 (tt0) REVERT: A 98 MET cc_start: 0.7402 (tpp) cc_final: 0.7074 (pmm) REVERT: A 166 TYR cc_start: 0.5061 (m-80) cc_final: 0.4227 (m-80) REVERT: A 204 MET cc_start: 0.7071 (mtt) cc_final: 0.6855 (mtt) REVERT: A 539 TYR cc_start: 0.4877 (m-10) cc_final: 0.4676 (m-10) REVERT: A 569 MET cc_start: 0.6800 (tmm) cc_final: 0.6253 (tmm) REVERT: A 620 ILE cc_start: 0.5681 (pt) cc_final: 0.5225 (tp) REVERT: A 890 GLU cc_start: 0.5008 (OUTLIER) cc_final: 0.4269 (tt0) REVERT: B 519 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7207 (mpp) REVERT: B 578 MET cc_start: 0.3542 (tmm) cc_final: 0.3053 (tpp) REVERT: C 93 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6085 (tptp) REVERT: D 107 PHE cc_start: 0.5074 (OUTLIER) cc_final: 0.3750 (m-10) REVERT: D 228 LEU cc_start: 0.8811 (mm) cc_final: 0.8604 (mm) REVERT: D 333 VAL cc_start: 0.9157 (t) cc_final: 0.8903 (p) REVERT: D 569 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6484 (ppp) REVERT: D 645 PHE cc_start: 0.4492 (t80) cc_final: 0.3813 (t80) REVERT: D 802 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7681 (ptt-90) REVERT: D 936 MET cc_start: 0.2183 (ppp) cc_final: 0.1187 (ptt) REVERT: D 979 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7845 (t-170) REVERT: E 936 MET cc_start: 0.1879 (mpt) cc_final: 0.1161 (mtt) REVERT: E 976 MET cc_start: 0.5569 (mmp) cc_final: 0.5227 (mmp) outliers start: 71 outliers final: 37 residues processed: 251 average time/residue: 0.4628 time to fit residues: 200.5471 Evaluate side-chains 210 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 802 ARG Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 931 GLU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 72 optimal weight: 2.9990 chunk 398 optimal weight: 5.9990 chunk 358 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 348 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.096736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.083482 restraints weight = 186832.675| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 4.50 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.8748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34350 Z= 0.143 Angle : 0.643 12.612 46282 Z= 0.336 Chirality : 0.042 0.217 4944 Planarity : 0.003 0.052 5890 Dihedral : 5.440 53.399 4428 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.53 % Favored : 92.11 % Rotamer: Outliers : 1.40 % Allowed : 14.59 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3982 helix: 0.52 (0.11), residues: 2388 sheet: -3.21 (0.33), residues: 180 loop : -2.17 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 919 HIS 0.009 0.001 HIS A 128 PHE 0.021 0.001 PHE D 916 TYR 0.029 0.002 TYR A 539 ARG 0.005 0.001 ARG D 566 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 1590) hydrogen bonds : angle 4.49744 ( 4542) covalent geometry : bond 0.00310 (34350) covalent geometry : angle 0.64299 (46282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.3421 (OUTLIER) cc_final: 0.2537 (tt0) REVERT: A 98 MET cc_start: 0.7710 (tpp) cc_final: 0.7361 (pmm) REVERT: A 166 TYR cc_start: 0.5199 (m-80) cc_final: 0.4451 (m-80) REVERT: A 167 LEU cc_start: 0.3893 (OUTLIER) cc_final: 0.3658 (tt) REVERT: A 204 MET cc_start: 0.6934 (mtt) cc_final: 0.6530 (mtt) REVERT: A 569 MET cc_start: 0.6638 (tmm) cc_final: 0.6154 (tmm) REVERT: A 620 ILE cc_start: 0.5797 (pt) cc_final: 0.5575 (tp) REVERT: A 866 MET cc_start: 0.6052 (tpp) cc_final: 0.5138 (tpp) REVERT: A 890 GLU cc_start: 0.5296 (OUTLIER) cc_final: 0.4597 (tt0) REVERT: B 519 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7098 (mpp) REVERT: B 578 MET cc_start: 0.3267 (tmm) cc_final: 0.2865 (tpp) REVERT: B 791 TYR cc_start: 0.5216 (OUTLIER) cc_final: 0.4923 (m-80) REVERT: C 93 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6229 (tptp) REVERT: D 107 PHE cc_start: 0.5355 (OUTLIER) cc_final: 0.4111 (m-10) REVERT: D 193 TYR cc_start: -0.0102 (t80) cc_final: -0.0791 (t80) REVERT: D 228 LEU cc_start: 0.8761 (mm) cc_final: 0.8525 (mm) REVERT: D 333 VAL cc_start: 0.9172 (t) cc_final: 0.8964 (p) REVERT: D 395 CYS cc_start: 0.7328 (p) cc_final: 0.7078 (p) REVERT: D 552 TYR cc_start: 0.7739 (t80) cc_final: 0.7481 (t80) REVERT: D 569 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6638 (ppp) REVERT: D 645 PHE cc_start: 0.4563 (t80) cc_final: 0.3972 (t80) REVERT: D 802 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7717 (ptt-90) REVERT: D 839 PHE cc_start: 0.6509 (t80) cc_final: 0.6105 (t80) REVERT: D 866 MET cc_start: 0.6588 (tpp) cc_final: 0.5718 (tpp) REVERT: D 936 MET cc_start: 0.2212 (ppp) cc_final: 0.1197 (ptt) REVERT: D 979 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7948 (t-170) REVERT: E 913 MET cc_start: 0.7151 (mmm) cc_final: 0.6838 (mmm) REVERT: E 936 MET cc_start: 0.1728 (mpt) cc_final: -0.0804 (ptm) outliers start: 52 outliers final: 30 residues processed: 220 average time/residue: 0.4380 time to fit residues: 161.3360 Evaluate side-chains 199 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 4.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 569 MET Chi-restraints excluded: chain D residue 802 ARG Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 48 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 349 optimal weight: 0.9990 chunk 296 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 307 optimal weight: 0.8980 chunk 396 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS B 614 ASN B 765 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 226 ASN D 487 GLN D 927 ASN D 973 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN ** E 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 698 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.091402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.078405 restraints weight = 186523.547| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 4.39 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 1.0007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 34350 Z= 0.262 Angle : 0.823 13.542 46282 Z= 0.432 Chirality : 0.048 0.305 4944 Planarity : 0.005 0.101 5890 Dihedral : 6.150 57.291 4428 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.07 % Favored : 89.58 % Rotamer: Outliers : 1.65 % Allowed : 14.46 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 3982 helix: -0.01 (0.11), residues: 2378 sheet: -3.18 (0.42), residues: 132 loop : -2.43 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 757 HIS 0.024 0.002 HIS A 128 PHE 0.045 0.003 PHE D 215 TYR 0.047 0.003 TYR E 896 ARG 0.010 0.001 ARG E 892 Details of bonding type rmsd hydrogen bonds : bond 0.05280 ( 1590) hydrogen bonds : angle 5.25569 ( 4542) covalent geometry : bond 0.00579 (34350) covalent geometry : angle 0.82252 (46282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 3.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.3927 (OUTLIER) cc_final: 0.3013 (tt0) REVERT: A 95 LYS cc_start: 0.7713 (tptm) cc_final: 0.7295 (mmtt) REVERT: A 98 MET cc_start: 0.7688 (tpp) cc_final: 0.7380 (pmm) REVERT: A 166 TYR cc_start: 0.5589 (m-80) cc_final: 0.5008 (m-80) REVERT: A 569 MET cc_start: 0.6726 (tmm) cc_final: 0.6360 (tmm) REVERT: A 890 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.4915 (tt0) REVERT: B 396 MET cc_start: 0.7181 (mmt) cc_final: 0.6628 (mmt) REVERT: B 551 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7282 (mt) REVERT: B 578 MET cc_start: 0.3309 (tmm) cc_final: 0.2908 (tpp) REVERT: C 93 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6741 (tptp) REVERT: D 46 VAL cc_start: 0.7848 (m) cc_final: 0.6801 (t) REVERT: D 107 PHE cc_start: 0.4929 (OUTLIER) cc_final: 0.3682 (m-10) REVERT: D 186 LYS cc_start: 0.1209 (OUTLIER) cc_final: 0.0269 (mmmt) REVERT: D 193 TYR cc_start: 0.0197 (t80) cc_final: -0.0390 (t80) REVERT: D 218 TYR cc_start: 0.1063 (m-80) cc_final: -0.0446 (t80) REVERT: D 395 CYS cc_start: 0.7599 (p) cc_final: 0.7232 (p) REVERT: D 434 ASP cc_start: 0.7584 (m-30) cc_final: 0.7264 (t0) REVERT: D 552 TYR cc_start: 0.7776 (t80) cc_final: 0.7434 (t80) REVERT: D 645 PHE cc_start: 0.4738 (t80) cc_final: 0.4081 (t80) REVERT: D 704 MET cc_start: 0.2882 (OUTLIER) cc_final: 0.1777 (mmm) REVERT: D 802 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7741 (ptt-90) REVERT: D 839 PHE cc_start: 0.6563 (t80) cc_final: 0.6170 (t80) REVERT: D 936 MET cc_start: 0.2184 (ppp) cc_final: 0.1298 (ptt) REVERT: D 979 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7979 (t-170) REVERT: E 704 MET cc_start: 0.5839 (tmm) cc_final: 0.5266 (tmm) outliers start: 61 outliers final: 31 residues processed: 242 average time/residue: 0.4363 time to fit residues: 175.9156 Evaluate side-chains 203 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 802 ARG Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 552 TYR Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 948 ASN Chi-restraints excluded: chain E residue 981 ILE Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 276 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 203 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 397 optimal weight: 10.0000 chunk 270 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN A 978 HIS B 992 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.094444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.081351 restraints weight = 187333.067| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 4.47 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 1.0014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34350 Z= 0.125 Angle : 0.671 14.342 46282 Z= 0.348 Chirality : 0.043 0.293 4944 Planarity : 0.003 0.058 5890 Dihedral : 5.579 54.595 4428 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.36 % Favored : 92.34 % Rotamer: Outliers : 0.84 % Allowed : 15.80 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 3982 helix: 0.48 (0.11), residues: 2348 sheet: -2.95 (0.45), residues: 122 loop : -2.28 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 958 HIS 0.006 0.001 HIS A 128 PHE 0.030 0.001 PHE E 522 TYR 0.035 0.002 TYR E 896 ARG 0.006 0.001 ARG B 10 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 1590) hydrogen bonds : angle 4.64829 ( 4542) covalent geometry : bond 0.00265 (34350) covalent geometry : angle 0.67112 (46282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 4.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.1318 (ppp) cc_final: 0.1030 (ppp) REVERT: A 59 TRP cc_start: 0.4166 (t-100) cc_final: 0.3031 (m-90) REVERT: A 68 GLU cc_start: 0.3865 (OUTLIER) cc_final: 0.2929 (tt0) REVERT: A 95 LYS cc_start: 0.7730 (tptm) cc_final: 0.7430 (mmtt) REVERT: A 98 MET cc_start: 0.7778 (tpp) cc_final: 0.7459 (pmm) REVERT: A 166 TYR cc_start: 0.5794 (m-80) cc_final: 0.5183 (m-80) REVERT: A 569 MET cc_start: 0.6555 (tmm) cc_final: 0.6213 (tmm) REVERT: A 853 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8416 (pp) REVERT: A 866 MET cc_start: 0.6057 (tpp) cc_final: 0.4996 (tpp) REVERT: A 890 GLU cc_start: 0.5669 (OUTLIER) cc_final: 0.4714 (tt0) REVERT: B 578 MET cc_start: 0.3265 (tmm) cc_final: 0.2892 (tpp) REVERT: C 93 LYS cc_start: 0.7293 (ptpp) cc_final: 0.6551 (tptp) REVERT: D 107 PHE cc_start: 0.5694 (OUTLIER) cc_final: 0.4416 (m-10) REVERT: D 215 PHE cc_start: 0.5468 (m-80) cc_final: 0.5082 (m-80) REVERT: D 434 ASP cc_start: 0.7491 (m-30) cc_final: 0.7214 (t0) REVERT: D 552 TYR cc_start: 0.7478 (t80) cc_final: 0.7249 (t80) REVERT: D 645 PHE cc_start: 0.4480 (t80) cc_final: 0.3873 (t80) REVERT: D 802 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7826 (ptt-90) REVERT: D 839 PHE cc_start: 0.6687 (t80) cc_final: 0.6363 (t80) REVERT: D 866 MET cc_start: 0.6386 (tpp) cc_final: 0.5453 (tpp) REVERT: D 936 MET cc_start: 0.1998 (ppp) cc_final: 0.1125 (ptt) REVERT: D 979 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.8084 (t-170) REVERT: E 11 TYR cc_start: 0.7293 (t80) cc_final: 0.6967 (t80) REVERT: E 357 MET cc_start: 0.7720 (mmp) cc_final: 0.7477 (mmt) REVERT: E 704 MET cc_start: 0.5877 (tmm) cc_final: 0.5302 (tmm) outliers start: 31 outliers final: 17 residues processed: 208 average time/residue: 0.4550 time to fit residues: 158.6221 Evaluate side-chains 181 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 5.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 802 ARG Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 361 optimal weight: 8.9990 chunk 358 optimal weight: 0.8980 chunk 346 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 362 optimal weight: 0.9990 chunk 178 optimal weight: 0.0370 chunk 347 optimal weight: 0.3980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN C 101 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.094560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.081473 restraints weight = 186895.682| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 4.46 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 1.0126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34350 Z= 0.120 Angle : 0.657 13.472 46282 Z= 0.339 Chirality : 0.043 0.427 4944 Planarity : 0.003 0.056 5890 Dihedral : 5.333 51.771 4428 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.18 % Favored : 92.52 % Rotamer: Outliers : 0.76 % Allowed : 15.97 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3982 helix: 0.64 (0.11), residues: 2372 sheet: -2.93 (0.39), residues: 146 loop : -2.14 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 25 HIS 0.020 0.001 HIS A 978 PHE 0.021 0.001 PHE E 522 TYR 0.033 0.001 TYR E 896 ARG 0.004 0.000 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1590) hydrogen bonds : angle 4.52048 ( 4542) covalent geometry : bond 0.00258 (34350) covalent geometry : angle 0.65706 (46282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13088.68 seconds wall clock time: 229 minutes 47.07 seconds (13787.07 seconds total)