Starting phenix.real_space_refine on Sat Jun 28 21:00:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3w_38902/06_2025/8y3w_38902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3w_38902/06_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_38902/06_2025/8y3w_38902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3w_38902/06_2025/8y3w_38902.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3w_38902/06_2025/8y3w_38902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3w_38902/06_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 19.97, 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: 7.78 Conformation dependent library (CDL) restraints added in 4.0 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: 4.07 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: 12.79 Time building geometry restraints manager: 9.36 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: 0.14 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 73.380 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.810 ------------------------------------------------------------------------------- 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 : 3.654 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: 0.5118 time to fit residues: 430.7260 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 : 3.580 ------------------------------------------------------------------------------- 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 = 65)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.096383 restraints weight = 196011.325| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 4.72 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 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 : 3.775 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: 0.7904 (mm-30) cc_final: 0.7626 (pt0) REVERT: A 59 TRP cc_start: 0.4925 (t-100) cc_final: 0.3548 (m-90) REVERT: A 68 GLU cc_start: 0.3046 (OUTLIER) cc_final: 0.2067 (tt0) REVERT: A 225 ILE cc_start: 0.8264 (mm) cc_final: 0.8061 (mt) REVERT: A 395 CYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5885 (p) REVERT: A 569 MET cc_start: 0.7135 (tmm) cc_final: 0.6050 (tmm) REVERT: A 601 TRP cc_start: 0.3921 (t-100) cc_final: 0.2939 (t-100) REVERT: A 676 ILE cc_start: 0.4193 (mm) cc_final: 0.3428 (mm) REVERT: A 771 ILE cc_start: 0.8088 (mm) cc_final: 0.7773 (tt) REVERT: A 853 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7336 (tt) REVERT: A 890 GLU cc_start: 0.3889 (OUTLIER) cc_final: 0.3343 (tt0) REVERT: A 978 HIS cc_start: 0.8561 (t-90) cc_final: 0.8299 (t-90) REVERT: B 470 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8266 (p) REVERT: B 791 TYR cc_start: 0.5214 (OUTLIER) cc_final: 0.4432 (m-80) REVERT: B 936 MET cc_start: 0.5637 (mpt) cc_final: 0.3738 (ppp) REVERT: D 84 TYR cc_start: 0.2045 (m-10) cc_final: 0.1499 (m-10) REVERT: D 242 LYS cc_start: 0.7449 (mtpt) cc_final: 0.7242 (mtpt) REVERT: D 259 ILE cc_start: 0.8653 (mt) cc_final: 0.8340 (mm) REVERT: D 548 ASN cc_start: 0.4526 (p0) cc_final: 0.4220 (m110) REVERT: D 696 THR cc_start: 0.6758 (m) cc_final: 0.6548 (p) REVERT: D 936 MET cc_start: 0.2086 (tmm) cc_final: 0.1070 (ptt) REVERT: E 238 ASP cc_start: 0.6156 (t0) cc_final: 0.5953 (t70) REVERT: E 531 MET cc_start: 0.8626 (mmm) cc_final: 0.7983 (mmt) REVERT: E 866 MET cc_start: 0.2475 (ttt) cc_final: 0.1990 (ttt) REVERT: E 936 MET cc_start: 0.1877 (mpt) cc_final: -0.0669 (ptm) REVERT: F 27 VAL cc_start: 0.6343 (OUTLIER) cc_final: 0.5935 (m) outliers start: 72 outliers final: 25 residues processed: 350 average time/residue: 0.4507 time to fit residues: 263.5725 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 : 3.728 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.9980 chunk 42 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 228 optimal weight: 10.0000 chunk 329 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 487 GLN A 591 ASN A 698 GLN A 829 GLN A 927 ASN B 67 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 391 ASN B 591 ASN B 658 HIS C 17 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN D 299 ASN D 391 ASN D 529 ASN D 698 GLN D 782 GLN D 829 GLN D 832 GLN E 391 ASN ** E 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 ASN E 591 ASN E 614 ASN E 658 HIS E 698 GLN E 797 ASN ** E 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.101804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.088101 restraints weight = 187397.970| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 4.66 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 34350 Z= 0.233 Angle : 0.794 12.777 46282 Z= 0.424 Chirality : 0.047 0.251 4944 Planarity : 0.005 0.053 5890 Dihedral : 6.495 59.280 4428 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.54 % Favored : 91.08 % Rotamer: Outliers : 2.43 % Allowed : 9.95 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -2.17 (0.12), residues: 3982 helix: -0.49 (0.10), residues: 2372 sheet: -3.40 (0.33), residues: 156 loop : -2.76 (0.14), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP F 25 HIS 0.014 0.001 HIS A 128 PHE 0.033 0.003 PHE D 45 TYR 0.034 0.003 TYR D 791 ARG 0.009 0.001 ARG A 613 Details of bonding type rmsd hydrogen bonds : bond 0.05393 ( 1590) hydrogen bonds : angle 5.11993 ( 4542) covalent geometry : bond 0.00477 (34350) covalent geometry : angle 0.79363 (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 338 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 248 time to evaluate : 3.910 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: A 68 GLU cc_start: 0.3592 (OUTLIER) cc_final: 0.2569 (tt0) REVERT: A 98 MET cc_start: 0.7491 (tpp) cc_final: 0.7241 (pmm) REVERT: A 225 ILE cc_start: 0.8904 (mm) cc_final: 0.8614 (mp) REVERT: A 291 ASP cc_start: 0.5987 (m-30) cc_final: 0.5690 (m-30) REVERT: A 297 GLN cc_start: 0.1302 (OUTLIER) cc_final: 0.0765 (pt0) REVERT: A 569 MET cc_start: 0.6896 (tmm) cc_final: 0.6191 (tmm) REVERT: A 645 PHE cc_start: 0.2743 (OUTLIER) cc_final: 0.2473 (t80) REVERT: A 771 ILE cc_start: 0.8336 (mm) cc_final: 0.8066 (tt) REVERT: A 787 ILE cc_start: 0.6500 (tt) cc_final: 0.6261 (pt) REVERT: A 863 ASN cc_start: 0.2120 (m110) cc_final: 0.1883 (t0) REVERT: A 871 ILE cc_start: 0.2706 (OUTLIER) cc_final: 0.2497 (mt) REVERT: A 890 GLU cc_start: 0.4080 (OUTLIER) cc_final: 0.3640 (tt0) REVERT: A 936 MET cc_start: 0.1446 (tmm) cc_final: 0.0656 (mpp) REVERT: A 978 HIS cc_start: 0.8684 (t-90) cc_final: 0.8333 (t-90) REVERT: B 523 ASN cc_start: 0.7559 (p0) cc_final: 0.7325 (p0) REVERT: B 791 TYR cc_start: 0.5786 (OUTLIER) cc_final: 0.4933 (m-80) REVERT: B 936 MET cc_start: 0.6075 (mpt) cc_final: 0.3832 (ptm) REVERT: D 84 TYR cc_start: 0.2555 (m-10) cc_final: 0.2339 (m-10) REVERT: D 107 PHE cc_start: 0.4841 (OUTLIER) cc_final: 0.3673 (m-10) REVERT: D 421 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7007 (ttm) REVERT: D 704 MET cc_start: 0.2033 (OUTLIER) cc_final: 0.0972 (mmm) REVERT: D 936 MET cc_start: 0.2553 (tmm) cc_final: 0.1844 (ptt) REVERT: D 976 MET cc_start: 0.2087 (tpp) cc_final: 0.1831 (tpp) REVERT: E 357 MET cc_start: 0.6754 (tpp) cc_final: 0.6488 (mmt) REVERT: E 396 MET cc_start: 0.7527 (mtt) cc_final: 0.7182 (mtt) REVERT: E 531 MET cc_start: 0.8889 (mmm) cc_final: 0.8225 (mmt) REVERT: E 563 ASN cc_start: 0.5427 (OUTLIER) cc_final: 0.5106 (m110) REVERT: E 833 LYS cc_start: 0.6777 (mttm) cc_final: 0.6573 (mmtm) REVERT: E 936 MET cc_start: 0.2000 (mpt) cc_final: -0.1572 (ptm) REVERT: E 976 MET cc_start: 0.5480 (OUTLIER) cc_final: 0.4998 (mmp) outliers start: 90 outliers final: 36 residues processed: 319 average time/residue: 0.4280 time to fit residues: 229.8153 Evaluate side-chains 236 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 3.671 ------------------------------------------------------------------------------- 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 228 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 469 CYS 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 871 ILE 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 691 ILE Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 PHE 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 421 MET Chi-restraints excluded: chain D residue 704 MET 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 563 ASN Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 931 GLU Chi-restraints excluded: chain E residue 976 MET Chi-restraints excluded: chain F residue 52 ARG 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: 0.9990 chunk 192 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 305 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 249 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 240 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 910 ASN A 979 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS E 829 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.101274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.087869 restraints weight = 190391.690| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 4.51 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34350 Z= 0.150 Angle : 0.657 12.172 46282 Z= 0.347 Chirality : 0.043 0.233 4944 Planarity : 0.004 0.064 5890 Dihedral : 5.988 55.025 4428 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.38 % Favored : 92.29 % Rotamer: Outliers : 1.97 % Allowed : 11.76 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -1.56 (0.13), residues: 3982 helix: 0.03 (0.11), residues: 2370 sheet: -3.15 (0.36), residues: 156 loop : -2.56 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 25 HIS 0.007 0.001 HIS A 658 PHE 0.030 0.002 PHE A 712 TYR 0.033 0.002 TYR A 539 ARG 0.007 0.001 ARG E 10 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 1590) hydrogen bonds : angle 4.67967 ( 4542) covalent geometry : bond 0.00322 (34350) covalent geometry : angle 0.65673 (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 302 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 229 time to evaluate : 3.551 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 68 GLU cc_start: 0.3587 (OUTLIER) cc_final: 0.2613 (tt0) REVERT: A 95 LYS cc_start: 0.8015 (tptp) cc_final: 0.7763 (mmtt) REVERT: A 98 MET cc_start: 0.7502 (tpp) cc_final: 0.7109 (pmm) REVERT: A 200 ILE cc_start: 0.5959 (mt) cc_final: 0.5658 (mm) REVERT: A 225 ILE cc_start: 0.9020 (mm) cc_final: 0.8697 (mp) REVERT: A 297 GLN cc_start: 0.1405 (OUTLIER) cc_final: 0.1065 (pt0) REVERT: A 531 MET cc_start: 0.2260 (tpp) cc_final: 0.1982 (tpp) REVERT: A 569 MET cc_start: 0.6998 (tmm) cc_final: 0.6363 (tmm) REVERT: A 645 PHE cc_start: 0.3017 (OUTLIER) cc_final: 0.2617 (t80) REVERT: A 787 ILE cc_start: 0.6562 (tt) cc_final: 0.6176 (pt) REVERT: A 792 SER cc_start: 0.5475 (t) cc_final: 0.5137 (p) REVERT: A 866 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4759 (mmp) REVERT: A 890 GLU cc_start: 0.4271 (OUTLIER) cc_final: 0.3748 (tt0) REVERT: A 936 MET cc_start: 0.1540 (tmm) cc_final: 0.0496 (mpp) REVERT: B 791 TYR cc_start: 0.5516 (OUTLIER) cc_final: 0.5043 (m-80) REVERT: D 356 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6783 (p90) REVERT: D 936 MET cc_start: 0.2377 (tmm) cc_final: 0.1727 (ptt) REVERT: D 976 MET cc_start: 0.2264 (tpp) cc_final: 0.2000 (tpp) REVERT: D 979 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7893 (t-170) REVERT: E 11 TYR cc_start: 0.7557 (t80) cc_final: 0.7314 (t80) REVERT: E 531 MET cc_start: 0.8774 (mmm) cc_final: 0.8110 (mmt) REVERT: E 936 MET cc_start: 0.1561 (mpt) cc_final: 0.0866 (mtt) outliers start: 73 outliers final: 32 residues processed: 288 average time/residue: 0.4165 time to fit residues: 202.8040 Evaluate side-chains 230 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 3.524 ------------------------------------------------------------------------------- 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 297 GLN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 866 MET 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 227 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 395 CYS 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 93 LYS Chi-restraints excluded: chain D residue 167 LEU 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 514 ARG Chi-restraints excluded: chain D residue 785 LYS Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 979 HIS 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 671 CYS Chi-restraints excluded: chain E residue 845 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 346 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 373 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 196 optimal weight: 8.9990 chunk 352 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 333 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 HIS A 391 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 HIS E 563 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.100855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.087436 restraints weight = 188449.085| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 4.53 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34350 Z= 0.124 Angle : 0.615 12.273 46282 Z= 0.324 Chirality : 0.041 0.238 4944 Planarity : 0.003 0.055 5890 Dihedral : 5.635 55.107 4428 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.13 % Favored : 92.52 % Rotamer: Outliers : 1.86 % Allowed : 12.94 % Favored : 85.19 % 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: -1.10 (0.13), residues: 3982 helix: 0.37 (0.11), residues: 2374 sheet: -3.02 (0.37), residues: 156 loop : -2.33 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 25 HIS 0.010 0.001 HIS D 128 PHE 0.022 0.001 PHE A 244 TYR 0.022 0.002 TYR A 471 ARG 0.008 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 1590) hydrogen bonds : angle 4.40166 ( 4542) covalent geometry : bond 0.00262 (34350) covalent geometry : angle 0.61499 (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 280 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 211 time to evaluate : 3.917 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: A 68 GLU cc_start: 0.3390 (OUTLIER) cc_final: 0.2555 (tt0) REVERT: A 98 MET cc_start: 0.7577 (tpp) cc_final: 0.7202 (pmm) REVERT: A 569 MET cc_start: 0.7149 (tmm) cc_final: 0.6260 (tmm) REVERT: A 619 LEU cc_start: 0.5554 (mt) cc_final: 0.5326 (mm) REVERT: A 792 SER cc_start: 0.5912 (t) cc_final: 0.5600 (p) REVERT: A 890 GLU cc_start: 0.4468 (OUTLIER) cc_final: 0.3975 (tt0) REVERT: A 936 MET cc_start: 0.1342 (tmm) cc_final: 0.0602 (mpp) REVERT: B 157 ASP cc_start: 0.7143 (m-30) cc_final: 0.6769 (m-30) REVERT: B 519 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6759 (mpp) REVERT: B 791 TYR cc_start: 0.5316 (OUTLIER) cc_final: 0.4964 (m-80) REVERT: C 93 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.5140 (tptp) REVERT: D 107 PHE cc_start: 0.4999 (OUTLIER) cc_final: 0.3700 (m-10) REVERT: D 421 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7007 (ttm) REVERT: D 877 PHE cc_start: -0.0808 (OUTLIER) cc_final: -0.1780 (p90) REVERT: D 936 MET cc_start: 0.1998 (tmm) cc_final: 0.1410 (ptt) REVERT: D 977 LYS cc_start: 0.5810 (OUTLIER) cc_final: 0.5575 (tptm) REVERT: D 979 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7809 (t-170) REVERT: E 531 MET cc_start: 0.8757 (mmm) cc_final: 0.8103 (mmt) REVERT: E 930 MET cc_start: 0.4333 (mpp) cc_final: 0.4130 (mpp) REVERT: E 931 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: E 936 MET cc_start: 0.1362 (mpt) cc_final: 0.0450 (mtt) REVERT: E 1001 MET cc_start: 0.3564 (tpp) cc_final: 0.3195 (tpp) outliers start: 69 outliers final: 28 residues processed: 267 average time/residue: 0.4420 time to fit residues: 196.8705 Evaluate side-chains 223 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 3.924 ------------------------------------------------------------------------------- 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 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 140 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 519 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 93 LYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 785 LYS 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 977 LYS 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 E residue 931 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 34 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 385 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 345 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 ASN A 765 ASN B 297 GLN D 58 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 765 ASN D 927 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 GLN E 563 ASN E 765 ASN E 978 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.096032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.082639 restraints weight = 182162.480| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 4.45 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.8270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34350 Z= 0.206 Angle : 0.733 12.787 46282 Z= 0.387 Chirality : 0.045 0.216 4944 Planarity : 0.004 0.054 5890 Dihedral : 5.991 53.930 4428 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.09 % Favored : 90.56 % Rotamer: Outliers : 2.37 % Allowed : 12.81 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.29 (0.13), residues: 3982 helix: 0.18 (0.11), residues: 2354 sheet: -2.94 (0.44), residues: 126 loop : -2.34 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 25 HIS 0.019 0.001 HIS A 128 PHE 0.032 0.002 PHE B 361 TYR 0.030 0.002 TYR D 313 ARG 0.007 0.001 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 1590) hydrogen bonds : angle 4.86881 ( 4542) covalent geometry : bond 0.00448 (34350) covalent geometry : angle 0.73325 (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 295 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 207 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.4318 (t-100) cc_final: 0.3042 (m-90) REVERT: A 68 GLU cc_start: 0.3798 (OUTLIER) cc_final: 0.2802 (tt0) REVERT: A 98 MET cc_start: 0.7555 (tpp) cc_final: 0.7263 (pmm) REVERT: A 507 PHE cc_start: 0.0870 (OUTLIER) cc_final: -0.0256 (m-80) REVERT: A 569 MET cc_start: 0.6828 (tmm) cc_final: 0.6246 (tmm) REVERT: A 792 SER cc_start: 0.6094 (t) cc_final: 0.5880 (p) REVERT: A 866 MET cc_start: 0.6474 (tpp) cc_final: 0.5696 (tpp) REVERT: A 890 GLU cc_start: 0.5198 (OUTLIER) cc_final: 0.4520 (tt0) REVERT: B 157 ASP cc_start: 0.7571 (m-30) cc_final: 0.7316 (m-30) REVERT: B 519 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7277 (mpp) REVERT: B 578 MET cc_start: 0.3836 (tmm) cc_final: 0.3323 (tpp) REVERT: C 93 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.5802 (tptp) REVERT: D 107 PHE cc_start: 0.4843 (OUTLIER) cc_final: 0.3580 (m-10) REVERT: D 386 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7262 (m-40) REVERT: D 421 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7263 (ttm) REVERT: D 514 ARG cc_start: 0.7260 (ptm160) cc_final: 0.6970 (ptm160) REVERT: D 802 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7756 (ptt-90) REVERT: D 979 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.7965 (t-170) REVERT: E 531 MET cc_start: 0.8748 (mmm) cc_final: 0.8178 (mmt) REVERT: E 866 MET cc_start: 0.4521 (ttt) cc_final: 0.4243 (ttt) REVERT: E 931 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: E 936 MET cc_start: 0.1738 (mpt) cc_final: 0.0975 (mtt) REVERT: F 114 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8608 (ttpp) outliers start: 88 outliers final: 39 residues processed: 280 average time/residue: 0.4456 time to fit residues: 207.6456 Evaluate side-chains 222 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 3.955 ------------------------------------------------------------------------------- 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 396 MET Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 551 LEU 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 227 MET Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 978 HIS 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 369 GLU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 561 LEU 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 869 ILE 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 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 555 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 931 GLU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 297 optimal weight: 7.9990 chunk 152 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 282 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 195 optimal weight: 0.0170 chunk 133 optimal weight: 1.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 992 ASN E 349 HIS E 563 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.097537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.084183 restraints weight = 186601.371| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 4.50 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.8425 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= 0.121 Angle : 0.629 12.308 46282 Z= 0.329 Chirality : 0.042 0.238 4944 Planarity : 0.003 0.056 5890 Dihedral : 5.595 54.031 4428 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.18 % Favored : 92.47 % Rotamer: Outliers : 1.56 % Allowed : 14.08 % Favored : 84.36 % 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: -0.99 (0.13), residues: 3982 helix: 0.48 (0.11), residues: 2360 sheet: -3.01 (0.35), residues: 180 loop : -2.26 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 143 HIS 0.008 0.001 HIS A 128 PHE 0.035 0.001 PHE A 839 TYR 0.036 0.001 TYR A 539 ARG 0.008 0.000 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 1590) hydrogen bonds : angle 4.49546 ( 4542) covalent geometry : bond 0.00257 (34350) covalent geometry : angle 0.62891 (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 246 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 3.907 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 59 TRP cc_start: 0.4220 (t-100) cc_final: 0.3111 (m-90) REVERT: A 68 GLU cc_start: 0.3524 (OUTLIER) cc_final: 0.2544 (tt0) REVERT: A 98 MET cc_start: 0.7649 (tpp) cc_final: 0.7238 (pmm) REVERT: A 166 TYR cc_start: 0.5051 (m-80) cc_final: 0.4406 (m-80) REVERT: A 569 MET cc_start: 0.6873 (tmm) cc_final: 0.6240 (tmm) REVERT: A 866 MET cc_start: 0.6429 (tpp) cc_final: 0.5786 (tpp) REVERT: A 890 GLU cc_start: 0.5175 (OUTLIER) cc_final: 0.4473 (tt0) REVERT: B 519 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7079 (mpp) REVERT: B 578 MET cc_start: 0.3320 (tmm) cc_final: 0.2882 (tpp) REVERT: C 93 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.5546 (tptp) REVERT: D 107 PHE cc_start: 0.5145 (OUTLIER) cc_final: 0.3830 (m-10) REVERT: D 300 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6192 (tppt) REVERT: D 363 LEU cc_start: 0.1841 (OUTLIER) cc_final: 0.1251 (tp) REVERT: D 514 ARG cc_start: 0.7288 (ptm160) cc_final: 0.7054 (ptm160) REVERT: D 552 TYR cc_start: 0.7746 (t80) cc_final: 0.7411 (t80) REVERT: D 936 MET cc_start: 0.2124 (ppp) cc_final: 0.1210 (ptt) REVERT: D 979 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7939 (t-170) REVERT: E 531 MET cc_start: 0.8774 (mmm) cc_final: 0.8573 (mmt) REVERT: E 866 MET cc_start: 0.4059 (ttt) cc_final: 0.3734 (ttt) REVERT: E 931 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: E 936 MET cc_start: 0.1497 (mpt) cc_final: -0.0876 (ptm) REVERT: E 1001 MET cc_start: 0.4081 (tpp) cc_final: 0.3775 (tpp) REVERT: F 52 ARG cc_start: 0.5313 (OUTLIER) cc_final: 0.5040 (ptt90) REVERT: F 114 LYS cc_start: 0.8893 (tmtt) cc_final: 0.8590 (ttpp) outliers start: 58 outliers final: 26 residues processed: 235 average time/residue: 0.5330 time to fit residues: 214.8036 Evaluate side-chains 208 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 3.869 ------------------------------------------------------------------------------- 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 105 LYS 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 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 519 MET Chi-restraints excluded: chain B residue 647 MET 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 300 LYS Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 561 LEU 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 563 ASN Chi-restraints excluded: chain E residue 618 LEU Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 931 GLU Chi-restraints excluded: chain F residue 20 ILE 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: 4.9990 chunk 398 optimal weight: 4.9990 chunk 358 optimal weight: 0.0030 chunk 195 optimal weight: 4.9990 chunk 348 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN ** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.096614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.083312 restraints weight = 186480.353| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 4.51 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.8780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34350 Z= 0.134 Angle : 0.638 12.593 46282 Z= 0.333 Chirality : 0.042 0.243 4944 Planarity : 0.003 0.059 5890 Dihedral : 5.486 52.840 4428 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.79 % Favored : 91.89 % Rotamer: Outliers : 1.65 % Allowed : 14.35 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.86 (0.14), residues: 3982 helix: 0.58 (0.11), residues: 2370 sheet: -2.92 (0.37), residues: 160 loop : -2.24 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 25 HIS 0.010 0.001 HIS A 128 PHE 0.025 0.001 PHE D 535 TYR 0.033 0.002 TYR D 261 ARG 0.007 0.001 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 1590) hydrogen bonds : angle 4.48526 ( 4542) covalent geometry : bond 0.00290 (34350) covalent geometry : angle 0.63834 (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 244 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 4.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.4211 (t-100) cc_final: 0.3019 (m-90) REVERT: A 68 GLU cc_start: 0.3612 (OUTLIER) cc_final: 0.2652 (tt0) REVERT: A 98 MET cc_start: 0.7592 (tpp) cc_final: 0.7279 (pmm) REVERT: A 166 TYR cc_start: 0.5032 (m-80) cc_final: 0.4296 (m-80) REVERT: A 569 MET cc_start: 0.6659 (tmm) cc_final: 0.6200 (tmm) REVERT: A 619 LEU cc_start: 0.6487 (mt) cc_final: 0.6029 (mm) REVERT: A 866 MET cc_start: 0.6644 (tpp) cc_final: 0.6091 (tpp) REVERT: A 890 GLU cc_start: 0.5307 (OUTLIER) cc_final: 0.4613 (tt0) REVERT: A 936 MET cc_start: 0.2293 (tmm) cc_final: 0.1099 (mpp) REVERT: B 71 TYR cc_start: 0.7045 (m-80) cc_final: 0.6765 (m-10) REVERT: B 519 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7234 (mpp) REVERT: B 578 MET cc_start: 0.3280 (tmm) cc_final: 0.2904 (tpp) REVERT: B 791 TYR cc_start: 0.5230 (OUTLIER) cc_final: 0.4939 (m-80) REVERT: C 93 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.5455 (tptp) REVERT: D 107 PHE cc_start: 0.5136 (OUTLIER) cc_final: 0.3872 (m-10) REVERT: D 193 TYR cc_start: -0.0216 (t80) cc_final: -0.0902 (t80) REVERT: D 514 ARG cc_start: 0.7226 (ptm160) cc_final: 0.6993 (ptm160) REVERT: D 552 TYR cc_start: 0.7778 (t80) cc_final: 0.7484 (t80) REVERT: D 647 MET cc_start: 0.7177 (mmm) cc_final: 0.6940 (mmt) REVERT: D 936 MET cc_start: 0.2147 (ppp) cc_final: 0.1147 (ptt) REVERT: D 979 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7934 (t-170) REVERT: E 11 TYR cc_start: 0.7224 (t80) cc_final: 0.6826 (t80) REVERT: E 531 MET cc_start: 0.8777 (mmm) cc_final: 0.8574 (mmt) REVERT: E 1001 MET cc_start: 0.3967 (tpp) cc_final: 0.3661 (tpp) REVERT: F 52 ARG cc_start: 0.5455 (OUTLIER) cc_final: 0.5129 (ptt90) REVERT: F 114 LYS cc_start: 0.8903 (tmtt) cc_final: 0.8617 (ttpp) outliers start: 61 outliers final: 29 residues processed: 233 average time/residue: 0.5202 time to fit residues: 207.7815 Evaluate side-chains 204 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 4.381 ------------------------------------------------------------------------------- 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 469 CYS Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 845 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 227 MET Chi-restraints excluded: chain B residue 444 CYS 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 C residue 93 LYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 561 LEU 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 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 563 ASN 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 20 ILE Chi-restraints excluded: chain F residue 52 ARG 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: 0.9990 chunk 248 optimal weight: 0.1980 chunk 349 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 307 optimal weight: 0.9980 chunk 396 optimal weight: 0.0670 chunk 169 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- 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 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.096455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.083162 restraints weight = 188675.942| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 4.54 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.9069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34350 Z= 0.127 Angle : 0.643 14.644 46282 Z= 0.334 Chirality : 0.042 0.343 4944 Planarity : 0.003 0.058 5890 Dihedral : 5.378 52.521 4428 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.31 % Favored : 92.37 % Rotamer: Outliers : 1.16 % Allowed : 15.02 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.78 (0.14), residues: 3982 helix: 0.65 (0.11), residues: 2372 sheet: -2.94 (0.37), residues: 160 loop : -2.21 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 958 HIS 0.009 0.001 HIS A 128 PHE 0.021 0.001 PHE D 45 TYR 0.045 0.002 TYR D 261 ARG 0.006 0.000 ARG D 566 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 1590) hydrogen bonds : angle 4.45226 ( 4542) covalent geometry : bond 0.00276 (34350) covalent geometry : angle 0.64336 (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 226 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.4050 (t-100) cc_final: 0.2858 (m-90) REVERT: A 68 GLU cc_start: 0.3448 (OUTLIER) cc_final: 0.2559 (tt0) REVERT: A 98 MET cc_start: 0.7657 (tpp) cc_final: 0.7308 (pmm) REVERT: A 166 TYR cc_start: 0.5237 (m-80) cc_final: 0.4658 (m-80) REVERT: A 515 ILE cc_start: 0.3292 (pt) cc_final: 0.2262 (tt) REVERT: A 569 MET cc_start: 0.6640 (tmm) cc_final: 0.6210 (tmm) REVERT: A 866 MET cc_start: 0.6491 (tpp) cc_final: 0.5966 (tpp) REVERT: A 890 GLU cc_start: 0.5464 (OUTLIER) cc_final: 0.4649 (tt0) REVERT: A 936 MET cc_start: 0.2077 (tmm) cc_final: 0.0916 (mpp) REVERT: B 71 TYR cc_start: 0.6946 (m-80) cc_final: 0.6681 (m-10) REVERT: B 519 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7203 (mpp) REVERT: B 578 MET cc_start: 0.3283 (tmm) cc_final: 0.2846 (tpp) REVERT: C 93 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.5669 (tptp) REVERT: D 107 PHE cc_start: 0.5463 (OUTLIER) cc_final: 0.4254 (m-10) REVERT: D 193 TYR cc_start: -0.0028 (t80) cc_final: -0.0782 (t80) REVERT: D 300 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6318 (tppt) REVERT: D 357 MET cc_start: 0.7506 (ttt) cc_final: 0.6727 (tmm) REVERT: D 395 CYS cc_start: 0.7255 (p) cc_final: 0.7010 (p) REVERT: D 514 ARG cc_start: 0.7184 (ptm160) cc_final: 0.6963 (ptm160) REVERT: D 552 TYR cc_start: 0.7733 (t80) cc_final: 0.7448 (t80) REVERT: D 802 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7776 (ptt-90) REVERT: D 936 MET cc_start: 0.2078 (ppp) cc_final: 0.1165 (ptt) REVERT: D 979 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7952 (t-170) REVERT: E 519 MET cc_start: 0.6702 (mmt) cc_final: 0.6472 (mmt) REVERT: E 866 MET cc_start: 0.3619 (ttt) cc_final: 0.3400 (ttt) REVERT: E 1001 MET cc_start: 0.3915 (tpp) cc_final: 0.3675 (tpp) REVERT: F 52 ARG cc_start: 0.5426 (OUTLIER) cc_final: 0.4967 (ptt90) REVERT: F 114 LYS cc_start: 0.8908 (tmtt) cc_final: 0.8607 (ttpp) outliers start: 43 outliers final: 27 residues processed: 215 average time/residue: 0.5099 time to fit residues: 185.1986 Evaluate side-chains 208 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 4.335 ------------------------------------------------------------------------------- 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 469 CYS Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 845 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 227 MET Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 647 MET 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 300 LYS Chi-restraints excluded: chain D residue 339 HIS Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 802 ARG Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 869 ILE 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 444 CYS Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 555 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 20 ILE Chi-restraints excluded: chain F residue 52 ARG 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: 0.7980 chunk 259 optimal weight: 8.9990 chunk 181 optimal weight: 0.7980 chunk 346 optimal weight: 0.0980 chunk 203 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 397 optimal weight: 0.6980 chunk 270 optimal weight: 0.3980 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.097116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.083907 restraints weight = 190286.253| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 4.53 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.9233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 34350 Z= 0.115 Angle : 0.637 14.762 46282 Z= 0.327 Chirality : 0.042 0.267 4944 Planarity : 0.003 0.058 5890 Dihedral : 5.239 51.311 4428 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.18 % Favored : 92.49 % Rotamer: Outliers : 1.11 % Allowed : 15.26 % Favored : 83.63 % 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: -0.59 (0.14), residues: 3982 helix: 0.80 (0.11), residues: 2350 sheet: -2.83 (0.37), residues: 160 loop : -2.08 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 958 HIS 0.010 0.001 HIS D 339 PHE 0.034 0.001 PHE E 360 TYR 0.033 0.001 TYR D 261 ARG 0.006 0.000 ARG D 566 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 1590) hydrogen bonds : angle 4.35959 ( 4542) covalent geometry : bond 0.00246 (34350) covalent geometry : angle 0.63691 (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 227 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 4.379 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: 0.3347 (OUTLIER) cc_final: 0.2477 (tt0) REVERT: A 98 MET cc_start: 0.7649 (tpp) cc_final: 0.7284 (pmm) REVERT: A 166 TYR cc_start: 0.5482 (m-80) cc_final: 0.5060 (m-80) REVERT: A 514 ARG cc_start: 0.7974 (ptm-80) cc_final: 0.7721 (ttp80) REVERT: A 515 ILE cc_start: 0.3939 (pt) cc_final: 0.3653 (tt) REVERT: A 569 MET cc_start: 0.6399 (tmm) cc_final: 0.6056 (tmm) REVERT: A 866 MET cc_start: 0.6759 (tpp) cc_final: 0.6261 (tpp) REVERT: A 878 THR cc_start: 0.3038 (OUTLIER) cc_final: 0.2732 (m) REVERT: A 890 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.4887 (tt0) REVERT: A 936 MET cc_start: 0.2054 (tmm) cc_final: 0.0956 (mpp) REVERT: B 9 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7688 (tptt) REVERT: B 71 TYR cc_start: 0.6893 (m-80) cc_final: 0.6668 (m-10) REVERT: B 578 MET cc_start: 0.3273 (tmm) cc_final: 0.2877 (tpp) REVERT: C 93 LYS cc_start: 0.6616 (OUTLIER) cc_final: 0.5739 (tptp) REVERT: D 107 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.4225 (m-10) REVERT: D 193 TYR cc_start: -0.0044 (t80) cc_final: -0.0737 (t80) REVERT: D 300 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6232 (tppt) REVERT: D 357 MET cc_start: 0.7510 (ttt) cc_final: 0.7171 (tmm) REVERT: D 395 CYS cc_start: 0.7394 (p) cc_final: 0.7181 (p) REVERT: D 514 ARG cc_start: 0.7227 (ptm160) cc_final: 0.7010 (ptm160) REVERT: D 552 TYR cc_start: 0.7730 (t80) cc_final: 0.7434 (t80) REVERT: D 936 MET cc_start: 0.2347 (ppp) cc_final: 0.1439 (ptt) REVERT: D 979 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7990 (t-170) REVERT: E 519 MET cc_start: 0.6715 (mmt) cc_final: 0.6402 (mmt) REVERT: E 866 MET cc_start: 0.3456 (ttt) cc_final: 0.3227 (ttt) REVERT: E 1001 MET cc_start: 0.3939 (tpp) cc_final: 0.3726 (tpp) REVERT: F 52 ARG cc_start: 0.5322 (OUTLIER) cc_final: 0.4926 (ptt90) outliers start: 41 outliers final: 21 residues processed: 217 average time/residue: 0.5078 time to fit residues: 188.1158 Evaluate side-chains 201 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 3.479 ------------------------------------------------------------------------------- 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 469 CYS Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 878 THR 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 227 MET Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 647 MET 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 300 LYS Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 52 ARG 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: 0.5980 chunk 358 optimal weight: 5.9990 chunk 346 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 362 optimal weight: 0.7980 chunk 178 optimal weight: 0.5980 chunk 347 optimal weight: 0.0370 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 698 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.097010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.083853 restraints weight = 190265.733| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 4.51 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.9379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 34350 Z= 0.114 Angle : 0.646 15.140 46282 Z= 0.329 Chirality : 0.042 0.304 4944 Planarity : 0.003 0.058 5890 Dihedral : 5.158 50.489 4428 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.08 % Favored : 92.59 % Rotamer: Outliers : 0.94 % Allowed : 15.59 % Favored : 83.47 % 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: -0.52 (0.14), residues: 3982 helix: 0.82 (0.11), residues: 2378 sheet: -2.81 (0.37), residues: 160 loop : -2.04 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 59 HIS 0.007 0.001 HIS A 128 PHE 0.030 0.001 PHE E 360 TYR 0.033 0.001 TYR D 261 ARG 0.011 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 1590) hydrogen bonds : angle 4.30573 ( 4542) covalent geometry : bond 0.00244 (34350) covalent geometry : angle 0.64583 (46282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14550.42 seconds wall clock time: 258 minutes 5.38 seconds (15485.38 seconds total)