Starting phenix.real_space_refine on Thu Nov 20 11:33:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3w_38902/11_2025/8y3w_38902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3w_38902/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y3w_38902/11_2025/8y3w_38902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3w_38902/11_2025/8y3w_38902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y3w_38902/11_2025/8y3w_38902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3w_38902/11_2025/8y3w_38902.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.035 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.06, per 1000 atoms: 0.24 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: 3.19 Conformation dependent library (CDL) restraints added in 1.4 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: 1.36 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: 6.96 Time building geometry restraints manager: 4.17 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: 0.06 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.760 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- 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 : 6.50 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.009 0.001 ARG A 480 TYR 0.052 0.003 TYR E 11 PHE 0.033 0.003 PHE A 839 TRP 0.054 0.004 TRP F 25 HIS 0.016 0.002 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00610 (34350) covalent geometry : angle 1.13717 (46282) hydrogen bonds : bond 0.17030 ( 1590) hydrogen bonds : angle 8.63088 ( 4542) *********************** 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 : 1.091 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: 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: 0.6666 (m-40) REVERT: A 661 ILE cc_start: 0.2101 (mp) cc_final: 0.1642 (pt) REVERT: A 676 ILE cc_start: 0.4364 (mm) cc_final: 0.3370 (mm) REVERT: A 757 TRP cc_start: 0.4509 (m-90) cc_final: 0.4072 (t-100) REVERT: A 978 HIS cc_start: 0.8462 (t-90) cc_final: 0.8242 (t-90) REVERT: B 124 MET cc_start: 0.7502 (mmm) cc_final: 0.7202 (mmm) REVERT: B 780 VAL cc_start: 0.8754 (t) cc_final: 0.7978 (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: 0.0561 (m) REVERT: D 84 TYR cc_start: 0.2881 (m-10) cc_final: 0.0879 (m-10) REVERT: D 167 LEU cc_start: 0.5812 (tt) cc_final: 0.5599 (tt) REVERT: D 548 ASN cc_start: 0.5386 (p0) cc_final: 0.4965 (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: 0.6614 (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: 0.2477 time to fit residues: 207.7450 Evaluate side-chains 256 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 252 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 845 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 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0570 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 overall best weight: 1.4106 ------------------------------------------------------------------------------- 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 614 ASN A 658 HIS A 698 GLN A 797 ASN A 863 ASN A 973 ASN A 992 ASN B 24 ASN B 171 HIS B 182 ASN B 211 HIS B 297 GLN B 391 ASN 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 B 658 HIS B 698 GLN B 829 GLN B 832 GLN B 939 GLN B 973 ASN B 990 ASN C 17 HIS C 21 ASN C 88 HIS D 24 ASN D 67 HIS D 171 HIS ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN D 467 ASN D 483 GLN D 658 HIS D 698 GLN D 782 GLN D 797 ASN D 990 ASN D 992 ASN E 24 ASN E 297 GLN E 391 ASN E 467 ASN E 521 ASN E 529 ASN E 591 ASN E 614 ASN E 698 GLN E 863 ASN E 973 ASN E 990 ASN F 17 HIS F 21 ASN F 88 HIS Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.107663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.094308 restraints weight = 193475.559| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 4.69 r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.3459 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= 0.162 Angle : 0.732 12.435 46282 Z= 0.390 Chirality : 0.044 0.257 4944 Planarity : 0.005 0.047 5890 Dihedral : 6.746 56.663 4431 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.01 % Favored : 92.52 % Rotamer: Outliers : 2.10 % Allowed : 8.20 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.12), residues: 3982 helix: -0.97 (0.10), residues: 2360 sheet: -3.49 (0.36), residues: 132 loop : -2.97 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 370 TYR 0.027 0.002 TYR B 940 PHE 0.044 0.002 PHE A 839 TRP 0.028 0.002 TRP F 25 HIS 0.008 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00342 (34350) covalent geometry : angle 0.73207 (46282) hydrogen bonds : bond 0.04722 ( 1590) hydrogen bonds : angle 5.21942 ( 4542) *********************** 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 375 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 297 time to evaluate : 1.431 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: 0.7899 (mm-30) cc_final: 0.7627 (pt0) REVERT: A 59 TRP cc_start: 0.4870 (t-100) cc_final: 0.3311 (m-90) REVERT: A 68 GLU cc_start: 0.3198 (OUTLIER) cc_final: 0.2223 (tt0) REVERT: A 225 ILE cc_start: 0.8426 (mm) cc_final: 0.8224 (mt) REVERT: A 227 MET cc_start: 0.4961 (OUTLIER) cc_final: 0.4537 (mtm) REVERT: A 569 MET cc_start: 0.7222 (tmm) cc_final: 0.6061 (tmm) REVERT: A 676 ILE cc_start: 0.4708 (mm) cc_final: 0.3978 (mm) REVERT: A 771 ILE cc_start: 0.8133 (mm) cc_final: 0.7801 (tt) REVERT: A 853 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7394 (tt) REVERT: A 890 GLU cc_start: 0.3943 (OUTLIER) cc_final: 0.3390 (tt0) REVERT: A 978 HIS cc_start: 0.8624 (t-90) cc_final: 0.8367 (t-90) REVERT: B 470 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8410 (p) REVERT: B 791 TYR cc_start: 0.5280 (OUTLIER) cc_final: 0.4480 (m-80) REVERT: B 936 MET cc_start: 0.5777 (mpt) cc_final: 0.3716 (ptm) REVERT: D 259 ILE cc_start: 0.8668 (mt) cc_final: 0.8353 (mm) REVERT: D 548 ASN cc_start: 0.5032 (p0) cc_final: 0.4412 (m110) REVERT: D 936 MET cc_start: 0.2034 (tmm) cc_final: 0.1086 (ptt) REVERT: E 238 ASP cc_start: 0.6332 (t0) cc_final: 0.6107 (t70) REVERT: E 357 MET cc_start: 0.6711 (tpp) cc_final: 0.6466 (mmt) REVERT: E 531 MET cc_start: 0.8711 (mmm) cc_final: 0.8109 (mmt) REVERT: F 27 VAL cc_start: 0.6567 (OUTLIER) cc_final: 0.6108 (m) outliers start: 78 outliers final: 27 residues processed: 357 average time/residue: 0.2145 time to fit residues: 127.2629 Evaluate side-chains 235 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 227 MET 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 469 CYS Chi-restraints excluded: chain A residue 560 GLU 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 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 215 PHE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 931 GLU Chi-restraints excluded: chain D residue 984 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 15 VAL 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 132 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 399 optimal weight: 7.9990 chunk 374 optimal weight: 20.0000 chunk 154 optimal weight: 0.9990 chunk 275 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 135 optimal weight: 0.0060 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 359 optimal weight: 0.9980 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 591 ASN B 523 ASN B 591 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN D 349 HIS D 386 ASN E 493 ASN E 591 ASN E 658 HIS E 797 ASN ** E 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.105933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.092336 restraints weight = 189865.170| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 4.69 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34350 Z= 0.141 Angle : 0.658 10.650 46282 Z= 0.349 Chirality : 0.043 0.249 4944 Planarity : 0.004 0.042 5890 Dihedral : 6.105 55.803 4429 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.26 % Favored : 92.34 % Rotamer: Outliers : 2.05 % Allowed : 9.98 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.13), residues: 3982 helix: -0.19 (0.10), residues: 2370 sheet: -3.40 (0.35), residues: 136 loop : -2.66 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 348 TYR 0.026 0.002 TYR D 338 PHE 0.029 0.002 PHE D 712 TRP 0.028 0.002 TRP F 25 HIS 0.005 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00300 (34350) covalent geometry : angle 0.65793 (46282) hydrogen bonds : bond 0.04276 ( 1590) hydrogen bonds : angle 4.70959 ( 4542) *********************** 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 303 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 227 time to evaluate : 1.411 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 28 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7573 (pt0) REVERT: A 68 GLU cc_start: 0.3327 (OUTLIER) cc_final: 0.2316 (tt0) REVERT: A 98 MET cc_start: 0.7657 (tpt) cc_final: 0.6987 (pmm) REVERT: A 225 ILE cc_start: 0.8622 (mm) cc_final: 0.8392 (mt) REVERT: A 560 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: A 569 MET cc_start: 0.6971 (tmm) cc_final: 0.6119 (tmm) REVERT: A 771 ILE cc_start: 0.8292 (mm) cc_final: 0.7974 (tt) REVERT: A 853 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7474 (tt) REVERT: A 890 GLU cc_start: 0.3824 (OUTLIER) cc_final: 0.3318 (tt0) REVERT: A 936 MET cc_start: 0.1573 (tmm) cc_final: 0.0499 (mpp) REVERT: A 978 HIS cc_start: 0.8644 (t-90) cc_final: 0.8420 (t-90) REVERT: B 519 MET cc_start: 0.7269 (mmm) cc_final: 0.6804 (tpp) REVERT: B 523 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7437 (p0) REVERT: B 563 ASN cc_start: 0.6767 (OUTLIER) cc_final: 0.6567 (p0) REVERT: B 791 TYR cc_start: 0.5418 (OUTLIER) cc_final: 0.4712 (m-80) REVERT: B 936 MET cc_start: 0.5872 (mpt) cc_final: 0.3625 (ptt) REVERT: D 60 TRP cc_start: 0.6199 (m-10) cc_final: 0.5787 (t60) REVERT: D 84 TYR cc_start: 0.2410 (m-10) cc_final: 0.1891 (m-10) REVERT: D 204 MET cc_start: 0.5234 (ptt) cc_final: 0.4999 (ptt) REVERT: D 225 ILE cc_start: 0.7583 (mm) cc_final: 0.7365 (mt) REVERT: D 515 ILE cc_start: 0.2073 (pt) cc_final: 0.1829 (pt) REVERT: D 936 MET cc_start: 0.2078 (tmm) cc_final: 0.1303 (ptt) REVERT: D 979 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7684 (t-90) REVERT: E 531 MET cc_start: 0.8724 (mmm) cc_final: 0.8110 (mmt) REVERT: E 866 MET cc_start: 0.2572 (ttt) cc_final: 0.2254 (ttt) REVERT: E 936 MET cc_start: 0.2199 (mtt) cc_final: -0.2287 (ptm) REVERT: E 976 MET cc_start: 0.5332 (OUTLIER) cc_final: 0.5063 (mmp) REVERT: F 73 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6722 (mt) outliers start: 76 outliers final: 33 residues processed: 288 average time/residue: 0.2096 time to fit residues: 101.7882 Evaluate side-chains 232 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 560 GLU 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 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 228 LEU Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 931 GLU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 976 MET Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 316 optimal weight: 6.9990 chunk 392 optimal weight: 10.0000 chunk 362 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 279 optimal weight: 0.9980 chunk 188 optimal weight: 0.2980 chunk 278 optimal weight: 1.9990 chunk 342 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 ASN A 698 GLN B 67 HIS B 523 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 386 ASN D 782 GLN E 563 ASN ** E 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.105031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.091574 restraints weight = 189410.201| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 4.57 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34350 Z= 0.121 Angle : 0.611 12.350 46282 Z= 0.321 Chirality : 0.041 0.233 4944 Planarity : 0.003 0.043 5890 Dihedral : 5.686 51.923 4428 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.83 % Favored : 92.82 % Rotamer: Outliers : 1.81 % Allowed : 10.71 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 3982 helix: 0.24 (0.11), residues: 2382 sheet: -3.29 (0.34), residues: 156 loop : -2.40 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 566 TYR 0.020 0.001 TYR E 223 PHE 0.020 0.001 PHE A 839 TRP 0.021 0.001 TRP F 25 HIS 0.006 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00254 (34350) covalent geometry : angle 0.61057 (46282) hydrogen bonds : bond 0.03718 ( 1590) hydrogen bonds : angle 4.41562 ( 4542) *********************** 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 282 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 215 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7567 (pt0) REVERT: A 68 GLU cc_start: 0.3485 (OUTLIER) cc_final: 0.2463 (tt0) REVERT: A 98 MET cc_start: 0.7617 (tpt) cc_final: 0.7298 (pmm) REVERT: A 225 ILE cc_start: 0.8714 (mm) cc_final: 0.8471 (mt) REVERT: A 291 ASP cc_start: 0.4681 (m-30) cc_final: 0.4360 (m-30) REVERT: A 316 ILE cc_start: 0.4477 (mm) cc_final: 0.4212 (mm) REVERT: A 569 MET cc_start: 0.6978 (tmm) cc_final: 0.6146 (tmm) REVERT: A 676 ILE cc_start: 0.6066 (mm) cc_final: 0.5780 (mm) REVERT: A 771 ILE cc_start: 0.8291 (mm) cc_final: 0.7988 (tt) REVERT: A 853 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7556 (tt) REVERT: A 890 GLU cc_start: 0.4205 (OUTLIER) cc_final: 0.3686 (tt0) REVERT: A 936 MET cc_start: 0.1463 (tmm) cc_final: 0.0663 (mpp) REVERT: A 976 MET cc_start: 0.5546 (ttt) cc_final: 0.5330 (ttt) REVERT: A 978 HIS cc_start: 0.8685 (t-90) cc_final: 0.8293 (t-90) REVERT: B 791 TYR cc_start: 0.5431 (OUTLIER) cc_final: 0.4991 (m-80) REVERT: B 936 MET cc_start: 0.6135 (mpt) cc_final: 0.3663 (ptt) REVERT: D 60 TRP cc_start: 0.6029 (m-10) cc_final: 0.5747 (t60) REVERT: D 84 TYR cc_start: 0.2362 (m-10) cc_final: 0.1285 (m-10) REVERT: D 107 PHE cc_start: 0.5017 (OUTLIER) cc_final: 0.3827 (m-10) REVERT: D 225 ILE cc_start: 0.8069 (mm) cc_final: 0.7743 (mt) REVERT: D 514 ARG cc_start: 0.7353 (ppt90) cc_final: 0.6966 (ppt170) REVERT: D 515 ILE cc_start: 0.3429 (pt) cc_final: 0.3005 (pt) REVERT: D 839 PHE cc_start: 0.6165 (t80) cc_final: 0.5889 (t80) REVERT: D 936 MET cc_start: 0.2111 (tmm) cc_final: 0.1432 (ptt) REVERT: D 979 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7808 (t-170) REVERT: E 531 MET cc_start: 0.8726 (mmm) cc_final: 0.7981 (mmt) REVERT: E 920 TYR cc_start: 0.6583 (t80) cc_final: 0.6374 (t80) REVERT: E 936 MET cc_start: 0.1795 (mtt) cc_final: 0.1442 (mtt) REVERT: E 942 PHE cc_start: 0.7536 (t80) cc_final: 0.7311 (t80) REVERT: E 976 MET cc_start: 0.5438 (mmp) cc_final: 0.5216 (mmp) REVERT: F 52 ARG cc_start: 0.4191 (OUTLIER) cc_final: 0.3820 (ptt90) REVERT: F 73 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6706 (mt) outliers start: 67 outliers final: 33 residues processed: 268 average time/residue: 0.2088 time to fit residues: 94.7076 Evaluate side-chains 222 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 839 PHE 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 563 ASN Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 931 GLU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 563 ASN Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 76 optimal weight: 3.9990 chunk 324 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 337 optimal weight: 9.9990 chunk 294 optimal weight: 0.2980 chunk 317 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 HIS A 910 ASN A 979 HIS ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN D 299 ASN D 529 ASN D 698 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.102272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.088703 restraints weight = 185922.008| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 4.56 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34350 Z= 0.146 Angle : 0.644 10.603 46282 Z= 0.340 Chirality : 0.042 0.229 4944 Planarity : 0.004 0.042 5890 Dihedral : 5.579 51.388 4428 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.66 % Favored : 91.99 % Rotamer: Outliers : 2.08 % Allowed : 11.60 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 3982 helix: 0.42 (0.11), residues: 2382 sheet: -3.17 (0.34), residues: 160 loop : -2.27 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 10 TYR 0.028 0.002 TYR E 11 PHE 0.031 0.002 PHE A 839 TRP 0.023 0.002 TRP F 25 HIS 0.008 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00315 (34350) covalent geometry : angle 0.64364 (46282) hydrogen bonds : bond 0.03998 ( 1590) hydrogen bonds : angle 4.45506 ( 4542) *********************** 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 292 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 215 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.3438 (OUTLIER) cc_final: 0.2522 (tt0) REVERT: A 98 MET cc_start: 0.7308 (tpt) cc_final: 0.6873 (pmm) REVERT: A 166 TYR cc_start: 0.4859 (m-80) cc_final: 0.4428 (m-80) REVERT: A 225 ILE cc_start: 0.8933 (mm) cc_final: 0.8654 (mp) REVERT: A 291 ASP cc_start: 0.4834 (m-30) cc_final: 0.4558 (m-30) REVERT: A 569 MET cc_start: 0.6881 (tmm) cc_final: 0.6043 (tmm) REVERT: A 771 ILE cc_start: 0.8388 (mm) cc_final: 0.8123 (tt) REVERT: A 792 SER cc_start: 0.4940 (t) cc_final: 0.4602 (p) REVERT: A 853 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 871 ILE cc_start: 0.3826 (OUTLIER) cc_final: 0.3584 (tt) REVERT: A 890 GLU cc_start: 0.4258 (OUTLIER) cc_final: 0.3721 (tt0) REVERT: A 936 MET cc_start: 0.1295 (tmm) cc_final: 0.0620 (mpp) REVERT: B 791 TYR cc_start: 0.5565 (OUTLIER) cc_final: 0.5049 (m-80) REVERT: D 107 PHE cc_start: 0.5124 (OUTLIER) cc_final: 0.3826 (m-10) REVERT: D 216 ILE cc_start: 0.6403 (mt) cc_final: 0.6196 (mm) REVERT: D 514 ARG cc_start: 0.7525 (ptt90) cc_final: 0.7021 (ppt170) REVERT: D 537 LYS cc_start: 0.3665 (tmtt) cc_final: 0.3299 (mmtt) REVERT: D 704 MET cc_start: 0.2238 (OUTLIER) cc_final: 0.1119 (mmm) REVERT: D 877 PHE cc_start: -0.1234 (OUTLIER) cc_final: -0.1887 (p90) REVERT: D 936 MET cc_start: 0.1940 (tmm) cc_final: 0.1399 (ptt) REVERT: D 979 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7720 (t-170) REVERT: E 519 MET cc_start: 0.6582 (mmt) cc_final: 0.6251 (mmt) REVERT: E 531 MET cc_start: 0.8741 (mmm) cc_final: 0.8103 (mmt) REVERT: E 920 TYR cc_start: 0.6396 (t80) cc_final: 0.6168 (t80) REVERT: E 976 MET cc_start: 0.5693 (OUTLIER) cc_final: 0.5091 (mmp) REVERT: F 73 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6826 (mt) outliers start: 77 outliers final: 38 residues processed: 271 average time/residue: 0.2111 time to fit residues: 95.9322 Evaluate side-chains 232 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 839 PHE 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 328 ILE Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 93 LYS 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 877 PHE Chi-restraints excluded: chain D residue 931 GLU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 706 VAL Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 976 MET Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 83 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 271 optimal weight: 6.9990 chunk 304 optimal weight: 3.9990 chunk 383 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 375 optimal weight: 0.4980 chunk 248 optimal weight: 10.0000 chunk 308 optimal weight: 0.8980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 224 ASN A 349 HIS A 391 ASN A 529 ASN A 765 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 HIS D 765 ASN E 202 ASN E 297 GLN ** E 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 698 GLN E 765 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.098065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.084651 restraints weight = 183235.610| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 4.44 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.7719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 34350 Z= 0.182 Angle : 0.706 18.401 46282 Z= 0.372 Chirality : 0.044 0.223 4944 Planarity : 0.004 0.065 5890 Dihedral : 5.766 52.817 4428 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.56 % Favored : 91.08 % Rotamer: Outliers : 1.97 % Allowed : 13.03 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 3982 helix: 0.34 (0.11), residues: 2380 sheet: -3.05 (0.40), residues: 136 loop : -2.29 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 870 TYR 0.026 0.002 TYR A 193 PHE 0.037 0.002 PHE E 942 TRP 0.026 0.002 TRP F 25 HIS 0.014 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00395 (34350) covalent geometry : angle 0.70559 (46282) hydrogen bonds : bond 0.04477 ( 1590) hydrogen bonds : angle 4.69799 ( 4542) *********************** 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 285 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 212 time to evaluate : 1.292 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: 0.3677 (OUTLIER) cc_final: 0.2795 (tt0) REVERT: A 98 MET cc_start: 0.7328 (tpt) cc_final: 0.7021 (pmm) REVERT: A 166 TYR cc_start: 0.5294 (m-80) cc_final: 0.4640 (m-80) REVERT: A 363 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6828 (tp) REVERT: A 378 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7293 (t80) REVERT: A 569 MET cc_start: 0.7208 (tmm) cc_final: 0.6689 (tmm) REVERT: A 789 GLN cc_start: 0.4639 (mm-40) cc_final: 0.4413 (mm-40) REVERT: A 871 ILE cc_start: 0.3977 (OUTLIER) cc_final: 0.3706 (mt) REVERT: A 890 GLU cc_start: 0.4890 (OUTLIER) cc_final: 0.4176 (tt0) REVERT: B 563 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.6728 (t0) REVERT: B 791 TYR cc_start: 0.5412 (OUTLIER) cc_final: 0.5010 (m-80) REVERT: C 93 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.5742 (tptp) REVERT: D 107 PHE cc_start: 0.5063 (OUTLIER) cc_final: 0.3716 (m-10) REVERT: D 216 ILE cc_start: 0.7514 (mt) cc_final: 0.7236 (mm) REVERT: D 434 ASP cc_start: 0.7448 (m-30) cc_final: 0.6912 (m-30) REVERT: D 771 ILE cc_start: 0.8871 (mm) cc_final: 0.8670 (tt) REVERT: D 936 MET cc_start: 0.1905 (tmm) cc_final: 0.1484 (ptt) REVERT: D 979 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.7793 (t-170) REVERT: E 531 MET cc_start: 0.8798 (mmm) cc_final: 0.8561 (mmt) REVERT: E 866 MET cc_start: 0.4522 (ttt) cc_final: 0.4225 (ttt) REVERT: E 976 MET cc_start: 0.5646 (OUTLIER) cc_final: 0.5416 (mmp) REVERT: F 114 LYS cc_start: 0.8919 (tmtt) cc_final: 0.8630 (ttpp) outliers start: 73 outliers final: 33 residues processed: 269 average time/residue: 0.2019 time to fit residues: 92.1057 Evaluate side-chains 229 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain A residue 378 TYR 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 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 227 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 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 931 GLU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 976 MET Chi-restraints excluded: chain F residue 83 ILE 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 386 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 377 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 222 optimal weight: 5.9990 chunk 390 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 287 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 226 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 HIS ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 992 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.096635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.083331 restraints weight = 184440.451| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 4.44 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.8462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 34350 Z= 0.175 Angle : 0.673 12.107 46282 Z= 0.354 Chirality : 0.044 0.259 4944 Planarity : 0.004 0.054 5890 Dihedral : 5.615 52.711 4428 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.94 % Favored : 91.74 % Rotamer: Outliers : 1.78 % Allowed : 14.13 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 3982 helix: 0.41 (0.11), residues: 2374 sheet: -3.03 (0.41), residues: 136 loop : -2.30 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 566 TYR 0.025 0.002 TYR D 920 PHE 0.022 0.002 PHE D 535 TRP 0.015 0.002 TRP C 25 HIS 0.011 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00383 (34350) covalent geometry : angle 0.67308 (46282) hydrogen bonds : bond 0.04210 ( 1590) hydrogen bonds : angle 4.62432 ( 4542) *********************** 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 262 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 196 time to evaluate : 1.363 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: 0.4065 (t-100) cc_final: 0.3082 (m-90) REVERT: A 68 GLU cc_start: 0.3586 (OUTLIER) cc_final: 0.2672 (tt0) REVERT: A 95 LYS cc_start: 0.7882 (tptm) cc_final: 0.7499 (mmtt) REVERT: A 98 MET cc_start: 0.7359 (tpt) cc_final: 0.6973 (pmm) REVERT: A 166 TYR cc_start: 0.5411 (m-80) cc_final: 0.4771 (m-80) REVERT: A 378 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7583 (t80) REVERT: A 569 MET cc_start: 0.7115 (tmm) cc_final: 0.6632 (tmm) REVERT: A 890 GLU cc_start: 0.5236 (OUTLIER) cc_final: 0.4561 (tt0) REVERT: A 936 MET cc_start: 0.2284 (ppp) cc_final: 0.0876 (mpp) REVERT: B 563 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.6744 (t0) REVERT: B 791 TYR cc_start: 0.5299 (OUTLIER) cc_final: 0.5019 (m-80) REVERT: C 93 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6160 (tptp) REVERT: D 107 PHE cc_start: 0.5228 (OUTLIER) cc_final: 0.3925 (m-10) REVERT: D 514 ARG cc_start: 0.7184 (ptt90) cc_final: 0.6906 (ppt170) REVERT: D 704 MET cc_start: 0.2871 (OUTLIER) cc_final: 0.1730 (mmm) REVERT: D 936 MET cc_start: 0.2040 (tmm) cc_final: 0.1668 (ptt) REVERT: D 979 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7861 (t-170) REVERT: E 531 MET cc_start: 0.8764 (mmm) cc_final: 0.8122 (mmt) REVERT: E 706 VAL cc_start: 0.6567 (OUTLIER) cc_final: 0.6361 (p) REVERT: E 976 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5388 (mmp) REVERT: F 114 LYS cc_start: 0.8933 (tmtt) cc_final: 0.8635 (ttpp) outliers start: 66 outliers final: 34 residues processed: 244 average time/residue: 0.2132 time to fit residues: 87.0984 Evaluate side-chains 212 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 200 ILE Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain 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 519 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 563 ASN 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 369 GLU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 561 LEU 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 931 GLU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 395 CYS 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 671 CYS Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 706 VAL Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 976 MET Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 83 ILE 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 185 optimal weight: 6.9990 chunk 293 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 355 optimal weight: 6.9990 chunk 309 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.095400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.082185 restraints weight = 185554.252| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 4.47 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.8993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34350 Z= 0.163 Angle : 0.684 12.636 46282 Z= 0.357 Chirality : 0.043 0.216 4944 Planarity : 0.004 0.068 5890 Dihedral : 5.567 51.890 4428 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.89 % Favored : 91.76 % Rotamer: Outliers : 1.67 % Allowed : 14.75 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 3982 helix: 0.48 (0.11), residues: 2358 sheet: -3.06 (0.41), residues: 136 loop : -2.30 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 566 TYR 0.021 0.002 TYR E 920 PHE 0.040 0.002 PHE D 645 TRP 0.025 0.002 TRP F 25 HIS 0.012 0.001 HIS A 979 Details of bonding type rmsd covalent geometry : bond 0.00357 (34350) covalent geometry : angle 0.68409 (46282) hydrogen bonds : bond 0.04198 ( 1590) hydrogen bonds : angle 4.69004 ( 4542) *********************** 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 251 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 1.376 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: 0.4222 (t-100) cc_final: 0.3065 (m-90) REVERT: A 68 GLU cc_start: 0.3497 (OUTLIER) cc_final: 0.2592 (tt0) REVERT: A 95 LYS cc_start: 0.7666 (tptm) cc_final: 0.7288 (mmtt) REVERT: A 98 MET cc_start: 0.7373 (tpt) cc_final: 0.6950 (pmm) REVERT: A 166 TYR cc_start: 0.5420 (m-80) cc_final: 0.4798 (m-80) REVERT: A 569 MET cc_start: 0.7081 (tmm) cc_final: 0.6673 (tmm) REVERT: A 713 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8415 (tp) REVERT: A 866 MET cc_start: 0.5500 (tpp) cc_final: 0.4773 (tpp) REVERT: A 890 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.4918 (tt0) REVERT: A 936 MET cc_start: 0.2373 (ppp) cc_final: 0.0880 (mpp) REVERT: B 563 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.6716 (t0) REVERT: B 791 TYR cc_start: 0.5303 (OUTLIER) cc_final: 0.4976 (m-80) REVERT: C 93 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6326 (tptp) REVERT: D 107 PHE cc_start: 0.5299 (OUTLIER) cc_final: 0.4007 (m-10) REVERT: D 228 LEU cc_start: 0.8848 (mm) cc_final: 0.8628 (mm) REVERT: D 802 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7848 (ptt-90) REVERT: D 936 MET cc_start: 0.1961 (tmm) cc_final: 0.1560 (ptt) REVERT: D 979 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7973 (t-170) REVERT: E 519 MET cc_start: 0.6943 (mmt) cc_final: 0.6702 (mmt) REVERT: E 531 MET cc_start: 0.8804 (mmm) cc_final: 0.8584 (mmt) REVERT: E 706 VAL cc_start: 0.6564 (OUTLIER) cc_final: 0.6361 (p) REVERT: E 976 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.5833 (mmp) outliers start: 62 outliers final: 29 residues processed: 234 average time/residue: 0.2151 time to fit residues: 84.5866 Evaluate side-chains 207 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 385 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 563 ASN 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 131 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 802 ARG Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 931 GLU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 706 VAL Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 976 MET Chi-restraints excluded: chain F residue 83 ILE 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 58 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 355 optimal weight: 6.9990 chunk 391 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.095326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.082163 restraints weight = 185661.904| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 4.49 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.9291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34350 Z= 0.140 Angle : 0.667 13.653 46282 Z= 0.345 Chirality : 0.043 0.216 4944 Planarity : 0.003 0.046 5890 Dihedral : 5.457 50.904 4428 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.61 % Favored : 92.06 % Rotamer: Outliers : 1.48 % Allowed : 14.94 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3982 helix: 0.65 (0.11), residues: 2336 sheet: -3.03 (0.41), residues: 138 loop : -2.23 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 514 TYR 0.030 0.002 TYR D 261 PHE 0.038 0.002 PHE D 645 TRP 0.015 0.001 TRP B 958 HIS 0.008 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00307 (34350) covalent geometry : angle 0.66658 (46282) hydrogen bonds : bond 0.03942 ( 1590) hydrogen bonds : angle 4.58964 ( 4542) *********************** 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 234 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 1.401 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 59 TRP cc_start: 0.4353 (t-100) cc_final: 0.3095 (m-90) REVERT: A 68 GLU cc_start: 0.3509 (OUTLIER) cc_final: 0.2652 (tt0) REVERT: A 98 MET cc_start: 0.7415 (tpt) cc_final: 0.6925 (pmm) REVERT: A 166 TYR cc_start: 0.5524 (m-80) cc_final: 0.4830 (m-80) REVERT: A 204 MET cc_start: 0.7754 (mtp) cc_final: 0.7540 (mtt) REVERT: A 378 TYR cc_start: 0.8313 (t80) cc_final: 0.8103 (t80) REVERT: A 515 ILE cc_start: 0.3704 (pt) cc_final: 0.2684 (tt) REVERT: A 560 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6875 (tm-30) REVERT: A 569 MET cc_start: 0.6998 (tmm) cc_final: 0.6532 (tmm) REVERT: A 866 MET cc_start: 0.5337 (tpp) cc_final: 0.4542 (tpp) REVERT: A 890 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.4933 (tt0) REVERT: A 936 MET cc_start: 0.2316 (ppp) cc_final: 0.0754 (mpp) REVERT: B 563 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.6742 (t0) REVERT: B 791 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.5012 (m-80) REVERT: C 93 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6310 (tptp) REVERT: D 107 PHE cc_start: 0.5231 (OUTLIER) cc_final: 0.3971 (m-10) REVERT: D 421 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.7036 (ttm) REVERT: D 531 MET cc_start: 0.3297 (mtp) cc_final: 0.3030 (mtp) REVERT: D 704 MET cc_start: 0.3209 (OUTLIER) cc_final: 0.2073 (mmm) REVERT: D 802 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7890 (ptt-90) REVERT: D 866 MET cc_start: 0.6333 (tpp) cc_final: 0.5480 (tpp) REVERT: D 936 MET cc_start: 0.2028 (tmm) cc_final: 0.1613 (ptt) REVERT: D 979 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.7884 (t-170) REVERT: E 531 MET cc_start: 0.8808 (mmm) cc_final: 0.8357 (mmt) REVERT: E 706 VAL cc_start: 0.6536 (OUTLIER) cc_final: 0.6315 (p) REVERT: E 866 MET cc_start: 0.3635 (ttt) cc_final: 0.3428 (ttt) REVERT: E 976 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.5854 (mmp) outliers start: 55 outliers final: 33 residues processed: 220 average time/residue: 0.2026 time to fit residues: 75.2801 Evaluate side-chains 212 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 385 PHE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 444 CYS Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 563 ASN 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 131 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 802 ARG Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 931 GLU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 671 CYS Chi-restraints excluded: chain E residue 704 MET Chi-restraints excluded: chain E residue 706 VAL Chi-restraints excluded: chain E residue 845 LEU Chi-restraints excluded: chain E residue 976 MET Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 16 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 293 optimal weight: 0.9990 chunk 362 optimal weight: 5.9990 chunk 305 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 226 ASN ** E 115 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 = 0.4379 r_free = 0.4379 target = 0.093841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.080692 restraints weight = 184652.060| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 4.47 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.9696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34350 Z= 0.159 Angle : 0.698 15.173 46282 Z= 0.360 Chirality : 0.044 0.228 4944 Planarity : 0.004 0.060 5890 Dihedral : 5.524 50.283 4428 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.99 % Favored : 91.69 % Rotamer: Outliers : 1.38 % Allowed : 15.16 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3982 helix: 0.60 (0.11), residues: 2348 sheet: -2.81 (0.45), residues: 122 loop : -2.21 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 514 TYR 0.034 0.002 TYR D 261 PHE 0.047 0.002 PHE A 839 TRP 0.020 0.002 TRP F 25 HIS 0.010 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00352 (34350) covalent geometry : angle 0.69798 (46282) hydrogen bonds : bond 0.04144 ( 1590) hydrogen bonds : angle 4.68770 ( 4542) ********************** 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 244 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.4538 (t-100) cc_final: 0.2997 (m-90) REVERT: A 68 GLU cc_start: 0.3568 (OUTLIER) cc_final: 0.2717 (tt0) REVERT: A 95 LYS cc_start: 0.7939 (tptm) cc_final: 0.7584 (mmtt) REVERT: A 98 MET cc_start: 0.7409 (tpt) cc_final: 0.6947 (pmm) REVERT: A 166 TYR cc_start: 0.5562 (m-80) cc_final: 0.4840 (m-80) REVERT: A 514 ARG cc_start: 0.7913 (ptm-80) cc_final: 0.7671 (ttp80) REVERT: A 515 ILE cc_start: 0.4211 (pt) cc_final: 0.3608 (tt) REVERT: A 569 MET cc_start: 0.6881 (tmm) cc_final: 0.6435 (tmm) REVERT: A 713 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8421 (tp) REVERT: A 866 MET cc_start: 0.5337 (tpp) cc_final: 0.4657 (tpp) REVERT: A 890 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.4841 (tt0) REVERT: C 93 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6421 (tptp) REVERT: D 107 PHE cc_start: 0.5602 (OUTLIER) cc_final: 0.4318 (m-10) REVERT: D 531 MET cc_start: 0.3297 (mtp) cc_final: 0.3059 (mtp) REVERT: D 704 MET cc_start: 0.3198 (OUTLIER) cc_final: 0.2059 (mmm) REVERT: D 802 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7751 (ptt-90) REVERT: D 866 MET cc_start: 0.6383 (tpp) cc_final: 0.5482 (tpp) REVERT: D 936 MET cc_start: 0.1582 (tmm) cc_final: 0.1200 (ptt) REVERT: D 979 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.7986 (t-170) REVERT: E 396 MET cc_start: 0.6640 (mtt) cc_final: 0.6227 (mtm) REVERT: E 519 MET cc_start: 0.7021 (mmt) cc_final: 0.6817 (mmt) REVERT: E 976 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6082 (mtt) outliers start: 51 outliers final: 30 residues processed: 229 average time/residue: 0.2102 time to fit residues: 81.0102 Evaluate side-chains 215 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 213 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 776 ASP 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 551 LEU 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 131 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 802 ARG Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 931 GLU Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 228 LEU 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 976 MET Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 223 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 305 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 383 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN A 910 ASN ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 927 ASN E 698 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.094635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.081605 restraints weight = 185104.397| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 4.44 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.9863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34350 Z= 0.126 Angle : 0.671 15.758 46282 Z= 0.343 Chirality : 0.043 0.316 4944 Planarity : 0.003 0.039 5890 Dihedral : 5.367 50.019 4428 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.23 % Favored : 92.47 % Rotamer: Outliers : 1.11 % Allowed : 15.48 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3982 helix: 0.77 (0.11), residues: 2334 sheet: -2.84 (0.39), residues: 146 loop : -2.15 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 514 TYR 0.025 0.001 TYR D 261 PHE 0.041 0.001 PHE D 645 TRP 0.022 0.001 TRP A 60 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00274 (34350) covalent geometry : angle 0.67099 (46282) hydrogen bonds : bond 0.03772 ( 1590) hydrogen bonds : angle 4.51192 ( 4542) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6789.36 seconds wall clock time: 118 minutes 16.23 seconds (7096.23 seconds total)