Starting phenix.real_space_refine on Fri May 30 11:09:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3y_38907/05_2025/8y3y_38907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3y_38907/05_2025/8y3y_38907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3y_38907/05_2025/8y3y_38907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3y_38907/05_2025/8y3y_38907.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3y_38907/05_2025/8y3y_38907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3y_38907/05_2025/8y3y_38907.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.031 sd= 0.084 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 44 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33586 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7968 Classifications: {'peptide': 957} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 937} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 7996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7996 Classifications: {'peptide': 958} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 938} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 829 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7968 Classifications: {'peptide': 957} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 937} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 7996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7996 Classifications: {'peptide': 958} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 938} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 829 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.08, per 1000 atoms: 0.54 Number of scatterers: 33586 At special positions: 0 Unit cell: (103.421, 128.199, 274.711, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 6292 8.00 N 5410 7.00 C 21754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.06 Conformation dependent library (CDL) restraints added in 3.9 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: 212 helices and 12 sheets defined 61.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.573A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.003A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.863A 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 95 through 109 removed outlier: 4.699A pdb=" N ALA A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.807A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.634A pdb=" N THR A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.662A pdb=" N VAL A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 160' Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.520A pdb=" N ASN A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 282 through 298 Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.830A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.918A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 373' Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.641A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 411 through 416' 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 462 removed outlier: 3.641A pdb=" N ILE A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 489 removed outlier: 4.795A pdb=" N SER A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 532 through 539 removed outlier: 3.632A pdb=" N LYS A 537 " --> pdb=" O PHE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 563 removed outlier: 3.679A pdb=" N GLU A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 4.369A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A 593 " --> pdb=" O TYR A 589 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.712A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.667A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.566A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 722 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.521A pdb=" N LEU A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 removed outlier: 4.454A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 784 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.806A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 831 through 841 Processing helix chain 'A' and resid 846 through 854 Processing helix chain 'A' and resid 878 through 895 removed outlier: 3.772A pdb=" N GLU A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 removed outlier: 4.164A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.623A pdb=" N ASP A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 973 through 991 removed outlier: 4.014A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.725A pdb=" N TYR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.798A pdb=" N LEU B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 removed outlier: 3.574A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 4.003A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.864A 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 95 through 109 removed outlier: 4.700A pdb=" N ALA B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.807A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.633A pdb=" N THR B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.662A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 160' Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.520A pdb=" N ASN B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 199 through 210 Processing helix chain 'B' and resid 222 through 235 Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 282 through 298 Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 321 removed outlier: 3.830A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 373 removed outlier: 3.918A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 371 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 373' Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.642A pdb=" N HIS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 411 through 416' 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 462 removed outlier: 3.641A pdb=" N ILE B 459 " --> pdb=" O TYR B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 493 removed outlier: 4.795A pdb=" N SER B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 527 through 531 Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.630A pdb=" N LYS B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 563 removed outlier: 3.679A pdb=" N GLU B 560 " --> pdb=" O VAL B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 598 removed outlier: 4.369A pdb=" N VAL B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 593 " --> pdb=" O TYR B 589 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.712A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.666A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.565A pdb=" N PHE B 659 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 670 Processing helix chain 'B' and resid 680 through 699 Processing helix chain 'B' and resid 705 through 722 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.521A pdb=" N LEU B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 removed outlier: 4.454A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 784 Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.806A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 831 through 841 Processing helix chain 'B' and resid 846 through 854 Processing helix chain 'B' and resid 878 through 895 removed outlier: 3.772A 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 929 through 933 Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.623A pdb=" N ASP B 945 " --> pdb=" O ASP B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 973 through 991 removed outlier: 4.015A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1003 removed outlier: 3.725A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.570A pdb=" N ASP C 13 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.583A pdb=" N ILE C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 23 through 39 removed outlier: 3.573A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 53 removed outlier: 4.003A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.865A 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 95 through 109 removed outlier: 4.700A pdb=" N ALA D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.807A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 removed outlier: 3.634A pdb=" N THR D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.663A pdb=" N VAL D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 160' Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.520A pdb=" N ASN D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 282 through 298 Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 321 removed outlier: 3.830A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 321' Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 366 through 373 removed outlier: 3.919A pdb=" N ARG D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER D 371 " --> pdb=" O CYS D 367 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 366 through 373' Processing helix chain 'D' and resid 374 through 391 Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.641A pdb=" N HIS D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 411 through 416' 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 462 removed outlier: 3.641A pdb=" N ILE D 459 " --> pdb=" O TYR D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 489 removed outlier: 4.795A pdb=" N SER D 474 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 527 through 531 Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.630A pdb=" N LYS D 537 " --> pdb=" O PHE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 563 removed outlier: 3.678A pdb=" N GLU D 560 " --> pdb=" O VAL D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 removed outlier: 4.370A pdb=" N VAL D 583 " --> pdb=" O SER D 579 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG D 593 " --> pdb=" O TYR D 589 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.711A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 628 removed outlier: 3.667A pdb=" N HIS D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 removed outlier: 3.566A pdb=" N PHE D 659 " --> pdb=" O ILE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 670 Processing helix chain 'D' and resid 680 through 699 Processing helix chain 'D' and resid 705 through 722 Processing helix chain 'D' and resid 723 through 725 No H-bonds generated for 'chain 'D' and resid 723 through 725' Processing helix chain 'D' and resid 729 through 742 removed outlier: 3.521A pdb=" N LEU D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 764 removed outlier: 4.454A pdb=" N CYS D 764 " --> pdb=" O ARG D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 784 Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.805A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 824 Processing helix chain 'D' and resid 831 through 841 Processing helix chain 'D' and resid 846 through 854 Processing helix chain 'D' and resid 878 through 895 removed outlier: 3.772A pdb=" N GLU D 882 " --> pdb=" O THR D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 922 removed outlier: 4.165A pdb=" N PHE D 916 " --> pdb=" O TYR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 933 Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.622A pdb=" N ASP D 945 " --> pdb=" O ASP D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 973 through 991 removed outlier: 4.014A pdb=" N HIS D 979 " --> pdb=" O HIS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1003 removed outlier: 3.725A pdb=" N TYR D1003 " --> pdb=" O ILE D 999 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 22 removed outlier: 4.106A pdb=" N LYS E 16 " --> pdb=" O GLY E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.572A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 53 removed outlier: 4.004A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.864A 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 95 through 109 removed outlier: 4.699A pdb=" N ALA E 99 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 122 removed outlier: 3.808A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 145 removed outlier: 3.634A pdb=" N THR E 140 " --> pdb=" O ASN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.663A pdb=" N VAL E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 154 through 160' Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.519A pdb=" N ASN E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 199 through 210 Processing helix chain 'E' and resid 222 through 235 Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 282 through 298 Processing helix chain 'E' and resid 304 through 317 Processing helix chain 'E' and resid 318 through 321 removed outlier: 3.829A pdb=" N ALA E 321 " --> pdb=" O PRO E 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 318 through 321' Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 355 through 366 Processing helix chain 'E' and resid 366 through 373 removed outlier: 3.919A pdb=" N ARG E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER E 371 " --> pdb=" O CYS E 367 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 366 through 373' Processing helix chain 'E' and resid 374 through 391 Processing helix chain 'E' and resid 411 through 416 removed outlier: 3.642A pdb=" N HIS E 415 " --> pdb=" O SER E 411 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 411 through 416' 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 462 removed outlier: 3.641A pdb=" N ILE E 459 " --> pdb=" O TYR E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 492 removed outlier: 4.795A pdb=" N SER E 474 " --> pdb=" O VAL E 470 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN E 475 " --> pdb=" O TYR E 471 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR E 490 " --> pdb=" O THR E 486 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN E 491 " --> pdb=" O GLN E 487 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE E 492 " --> pdb=" O ALA E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 519 Processing helix chain 'E' and resid 527 through 531 Processing helix chain 'E' and resid 532 through 539 removed outlier: 3.631A pdb=" N LYS E 537 " --> pdb=" O PHE E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 563 removed outlier: 3.679A pdb=" N GLU E 560 " --> pdb=" O VAL E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 598 removed outlier: 4.370A pdb=" N VAL E 583 " --> pdb=" O SER E 579 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG E 593 " --> pdb=" O TYR E 589 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN E 598 " --> pdb=" O PHE E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 removed outlier: 3.711A pdb=" N VAL E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 628 removed outlier: 3.667A pdb=" N HIS E 609 " --> pdb=" O PHE E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 659 removed outlier: 3.566A pdb=" N PHE E 659 " --> pdb=" O ILE E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 670 Processing helix chain 'E' and resid 680 through 699 Processing helix chain 'E' and resid 705 through 722 Processing helix chain 'E' and resid 723 through 725 No H-bonds generated for 'chain 'E' and resid 723 through 725' Processing helix chain 'E' and resid 729 through 742 removed outlier: 3.521A pdb=" N LEU E 733 " --> pdb=" O SER E 729 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 764 removed outlier: 4.454A pdb=" N CYS E 764 " --> pdb=" O ARG E 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 769 through 784 Processing helix chain 'E' and resid 800 through 812 removed outlier: 3.806A pdb=" N TYR E 804 " --> pdb=" O TYR E 800 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 824 Processing helix chain 'E' and resid 831 through 841 Processing helix chain 'E' and resid 846 through 854 Processing helix chain 'E' and resid 878 through 895 removed outlier: 3.771A 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 929 through 933 Processing helix chain 'E' and resid 937 through 945 removed outlier: 3.623A pdb=" N ASP E 945 " --> pdb=" O ASP E 941 " (cutoff:3.500A) Processing helix chain 'E' and resid 950 through 954 Processing helix chain 'E' and resid 973 through 991 removed outlier: 4.014A pdb=" N HIS E 979 " --> pdb=" O HIS E 975 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1003 removed outlier: 3.724A pdb=" N TYR E1003 " --> pdb=" O ILE E 999 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 14 removed outlier: 3.570A pdb=" N ASP F 13 " --> pdb=" O ALA F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 106 removed outlier: 3.582A pdb=" N ILE F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 7.089A pdb=" N VAL A 129 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 removed outlier: 7.089A pdb=" N VAL B 129 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'C' and resid 27 through 30 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: 7.089A pdb=" N VAL D 129 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 152 removed outlier: 7.088A pdb=" N VAL E 129 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE E 130 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE E 44 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE E 213 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE E 246 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE E 215 " --> pdb=" O ILE E 246 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'F' and resid 27 through 30 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 46 1560 hydrogen bonds defined for protein. 4584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.18 Time building geometry restraints manager: 8.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5628 1.31 - 1.43: 9586 1.43 - 1.56: 18919 1.56 - 1.69: 1 1.69 - 1.81: 216 Bond restraints: 34350 Sorted by residual: bond pdb=" C LEU A 842 " pdb=" N PRO A 843 " ideal model delta sigma weight residual 1.337 1.380 -0.043 9.80e-03 1.04e+04 1.93e+01 bond pdb=" C LEU E 842 " pdb=" N PRO E 843 " ideal model delta sigma weight residual 1.337 1.379 -0.043 9.80e-03 1.04e+04 1.89e+01 bond pdb=" C LEU B 842 " pdb=" N PRO B 843 " ideal model delta sigma weight residual 1.337 1.379 -0.043 9.80e-03 1.04e+04 1.89e+01 bond pdb=" C LEU D 842 " pdb=" N PRO D 843 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.86e+01 bond pdb=" C VAL A 565 " pdb=" N ARG A 566 " ideal model delta sigma weight residual 1.333 1.378 -0.045 1.36e-02 5.41e+03 1.09e+01 ... (remaining 34345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 45063 2.96 - 5.92: 1096 5.92 - 8.87: 106 8.87 - 11.83: 12 11.83 - 14.79: 5 Bond angle restraints: 46282 Sorted by residual: angle pdb=" CA GLN D 377 " pdb=" CB GLN D 377 " pdb=" CG GLN D 377 " ideal model delta sigma weight residual 114.10 101.81 12.29 2.00e+00 2.50e-01 3.78e+01 angle pdb=" N GLY C 70 " pdb=" CA GLY C 70 " pdb=" C GLY C 70 " ideal model delta sigma weight residual 112.08 105.99 6.09 1.01e+00 9.80e-01 3.63e+01 angle pdb=" N GLY F 70 " pdb=" CA GLY F 70 " pdb=" C GLY F 70 " ideal model delta sigma weight residual 112.08 106.04 6.04 1.01e+00 9.80e-01 3.58e+01 angle pdb=" N VAL C 32 " pdb=" CA VAL C 32 " pdb=" C VAL C 32 " ideal model delta sigma weight residual 113.20 107.46 5.74 9.60e-01 1.09e+00 3.58e+01 angle pdb=" N VAL F 32 " pdb=" CA VAL F 32 " pdb=" C VAL F 32 " ideal model delta sigma weight residual 113.20 107.47 5.73 9.60e-01 1.09e+00 3.57e+01 ... (remaining 46277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 18857 14.99 - 29.99: 1218 29.99 - 44.98: 351 44.98 - 59.97: 39 59.97 - 74.96: 9 Dihedral angle restraints: 20474 sinusoidal: 8496 harmonic: 11978 Sorted by residual: dihedral pdb=" CA SER B 957 " pdb=" C SER B 957 " pdb=" N TRP B 958 " pdb=" CA TRP B 958 " ideal model delta harmonic sigma weight residual 180.00 117.73 62.27 0 5.00e+00 4.00e-02 1.55e+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 180.00 117.74 62.26 0 5.00e+00 4.00e-02 1.55e+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 180.00 117.74 62.26 0 5.00e+00 4.00e-02 1.55e+02 ... (remaining 20471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4099 0.073 - 0.146: 735 0.146 - 0.219: 85 0.219 - 0.292: 17 0.292 - 0.364: 8 Chirality restraints: 4944 Sorted by residual: chirality pdb=" CG LEU D 330 " pdb=" CB LEU D 330 " pdb=" CD1 LEU D 330 " pdb=" CD2 LEU D 330 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CG LEU B 330 " pdb=" CB LEU B 330 " pdb=" CD1 LEU B 330 " pdb=" CD2 LEU B 330 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CG LEU E 330 " pdb=" CB LEU E 330 " pdb=" CD1 LEU E 330 " pdb=" CD2 LEU E 330 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 4941 not shown) Planarity restraints: 5890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 631 " -0.024 2.00e-02 2.50e+03 4.79e-02 2.30e+01 pdb=" C ILE E 631 " 0.083 2.00e-02 2.50e+03 pdb=" O ILE E 631 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP E 632 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 16 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C TYR F 16 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR F 16 " 0.024 2.00e-02 2.50e+03 pdb=" N HIS F 17 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 16 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C TYR C 16 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR C 16 " -0.024 2.00e-02 2.50e+03 pdb=" N HIS C 17 " -0.021 2.00e-02 2.50e+03 ... (remaining 5887 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1840 2.71 - 3.26: 33504 3.26 - 3.81: 54417 3.81 - 4.35: 69343 4.35 - 4.90: 113098 Nonbonded interactions: 272202 Sorted by model distance: nonbonded pdb=" O ASN A 563 " pdb=" N ARG A 566 " model vdw 2.168 3.120 nonbonded pdb=" OE1 GLN D 236 " pdb=" OG SER D 239 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLN B 236 " pdb=" OG SER B 239 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLN A 236 " pdb=" OG SER A 239 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLN E 236 " pdb=" OG SER E 239 " model vdw 2.215 3.040 ... (remaining 272197 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: 0.07 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: 3.280 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: 1.180 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 68.200 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4786 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 : 0.007 0.094 34350 Z= 0.334 Angle : 1.113 14.791 46282 Z= 0.667 Chirality : 0.059 0.364 4944 Planarity : 0.007 0.057 5890 Dihedral : 11.181 74.965 12762 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.44 % Favored : 91.19 % Rotamer: Outliers : 0.67 % Allowed : 4.05 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.10), residues: 3982 helix: -2.62 (0.08), residues: 2380 sheet: -4.65 (0.31), residues: 68 loop : -3.32 (0.13), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.005 TRP C 25 HIS 0.009 0.002 HIS B 786 PHE 0.027 0.003 PHE D 722 TYR 0.025 0.003 TYR D 574 ARG 0.024 0.001 ARG B 478 Details of bonding type rmsd hydrogen bonds : bond 0.17684 ( 1560) hydrogen bonds : angle 8.36203 ( 4584) covalent geometry : bond 0.00726 (34350) covalent geometry : angle 1.11332 (46282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 463 time to evaluate : 3.715 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: A 232 VAL cc_start: 0.6358 (m) cc_final: 0.5983 (p) REVERT: A 913 MET cc_start: -0.0069 (mmm) cc_final: -0.0347 (ttt) REVERT: B 124 MET cc_start: 0.8626 (mmm) cc_final: 0.8377 (mmm) REVERT: B 781 LEU cc_start: 0.8681 (tp) cc_final: 0.8448 (mt) REVERT: B 789 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7989 (mm110) REVERT: B 883 GLU cc_start: 0.9053 (tp30) cc_final: 0.8630 (mm-30) REVERT: B 920 TYR cc_start: 0.8108 (t80) cc_final: 0.7744 (t80) REVERT: B 922 LEU cc_start: 0.8919 (mm) cc_final: 0.8545 (mm) REVERT: B 930 MET cc_start: 0.8142 (mpt) cc_final: 0.7517 (mmm) REVERT: B 943 PHE cc_start: 0.8007 (m-80) cc_final: 0.7620 (m-80) REVERT: C 93 LYS cc_start: 0.8137 (mmpt) cc_final: 0.7520 (tptp) REVERT: C 98 ILE cc_start: 0.8933 (mt) cc_final: 0.8708 (mm) REVERT: C 102 LEU cc_start: 0.8214 (mt) cc_final: 0.7855 (mt) REVERT: D 21 MET cc_start: 0.3803 (mtm) cc_final: 0.2319 (tpp) REVERT: D 169 LYS cc_start: 0.4530 (mttt) cc_final: 0.3561 (mttp) REVERT: D 913 MET cc_start: 0.1886 (mmm) cc_final: 0.0952 (mmt) REVERT: E 699 PHE cc_start: 0.5787 (m-80) cc_final: 0.5513 (t80) REVERT: E 936 MET cc_start: 0.1366 (mpt) cc_final: 0.1072 (mpt) outliers start: 25 outliers final: 2 residues processed: 486 average time/residue: 0.4777 time to fit residues: 362.0952 Evaluate side-chains 269 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 267 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain E residue 859 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 1.9990 chunk 303 optimal weight: 0.0040 chunk 168 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 313 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 233 optimal weight: 7.9990 chunk 363 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 410 ASN A 483 GLN A 614 ASN A 702 ASN A 711 GLN A 765 ASN A 881 HIS B 93 ASN B 195 GLN B 351 ASN B 391 ASN B 711 GLN B 765 ASN B 829 GLN B 863 ASN B 975 HIS B 992 ASN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 88 HIS D 93 ASN D 666 ASN D 711 GLN D 765 ASN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 391 ASN E 711 GLN E 765 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.130621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.113917 restraints weight = 173228.784| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 5.07 r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34350 Z= 0.137 Angle : 0.641 10.695 46282 Z= 0.347 Chirality : 0.043 0.205 4944 Planarity : 0.004 0.061 5890 Dihedral : 6.543 56.003 4426 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.28 % Favored : 93.40 % Rotamer: Outliers : 1.62 % Allowed : 8.12 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.12), residues: 3982 helix: -1.18 (0.10), residues: 2442 sheet: -4.53 (0.31), residues: 68 loop : -3.08 (0.13), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 231 HIS 0.006 0.001 HIS A 881 PHE 0.031 0.002 PHE E 699 TYR 0.045 0.002 TYR E 709 ARG 0.020 0.001 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 1560) hydrogen bonds : angle 5.17162 ( 4584) covalent geometry : bond 0.00288 (34350) covalent geometry : angle 0.64133 (46282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 302 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8198 (mpp) cc_final: 0.7666 (mpp) REVERT: A 261 TYR cc_start: 0.7067 (m-10) cc_final: 0.6660 (m-80) REVERT: A 555 THR cc_start: 0.6822 (OUTLIER) cc_final: 0.6569 (m) REVERT: A 704 MET cc_start: 0.2200 (tpp) cc_final: 0.0889 (mmm) REVERT: A 705 ASN cc_start: 0.5915 (t0) cc_final: 0.5661 (p0) REVERT: B 930 MET cc_start: 0.7342 (mpt) cc_final: 0.7039 (mmm) REVERT: B 958 TRP cc_start: 0.6827 (m-10) cc_final: 0.6491 (m-10) REVERT: C 79 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6605 (m-80) REVERT: C 93 LYS cc_start: 0.7464 (mmpt) cc_final: 0.7023 (tptp) REVERT: D 169 LYS cc_start: 0.4864 (mttt) cc_final: 0.4544 (mttp) REVERT: D 389 GLU cc_start: 0.5791 (mt-10) cc_final: 0.5389 (mp0) REVERT: D 421 MET cc_start: 0.1196 (ttm) cc_final: 0.0921 (ttm) REVERT: D 555 THR cc_start: 0.5661 (OUTLIER) cc_final: 0.5386 (p) REVERT: D 647 MET cc_start: 0.1100 (tpt) cc_final: 0.0886 (tpt) REVERT: D 913 MET cc_start: 0.2493 (mmm) cc_final: 0.1942 (mmt) REVERT: E 522 PHE cc_start: 0.6645 (t80) cc_final: 0.6405 (t80) REVERT: E 531 MET cc_start: 0.8406 (mmm) cc_final: 0.7490 (mmm) REVERT: E 704 MET cc_start: 0.4506 (ppp) cc_final: 0.4276 (ppp) REVERT: E 841 LEU cc_start: 0.8181 (tp) cc_final: 0.7857 (mm) REVERT: E 930 MET cc_start: 0.1588 (mtt) cc_final: 0.1285 (mtm) REVERT: E 936 MET cc_start: 0.1590 (mpt) cc_final: 0.1239 (mpt) REVERT: E 1001 MET cc_start: 0.0717 (mtp) cc_final: -0.0072 (mtt) REVERT: F 81 PHE cc_start: 0.5197 (t80) cc_final: 0.4924 (t80) outliers start: 60 outliers final: 17 residues processed: 352 average time/residue: 0.4477 time to fit residues: 255.6903 Evaluate side-chains 238 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain D residue 736 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 168 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 240 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 329 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS A 351 ASN A 477 ASN A 614 ASN A 666 ASN A 702 ASN A 863 ASN A1002 ASN B 211 HIS B 658 HIS ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN D 391 ASN ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN E 351 ASN E 609 HIS E 658 HIS ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.123308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.108634 restraints weight = 168496.608| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 3.53 r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 34350 Z= 0.192 Angle : 0.702 13.252 46282 Z= 0.375 Chirality : 0.045 0.265 4944 Planarity : 0.005 0.056 5890 Dihedral : 6.130 51.149 4426 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.21 % Favored : 91.56 % Rotamer: Outliers : 2.16 % Allowed : 9.76 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.12), residues: 3982 helix: -0.57 (0.10), residues: 2422 sheet: -3.90 (0.36), residues: 96 loop : -2.77 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 919 HIS 0.008 0.001 HIS A 118 PHE 0.031 0.002 PHE A 608 TYR 0.039 0.002 TYR D 482 ARG 0.009 0.001 ARG D 478 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 1560) hydrogen bonds : angle 4.89719 ( 4584) covalent geometry : bond 0.00426 (34350) covalent geometry : angle 0.70174 (46282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 285 time to evaluate : 3.974 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: A 105 LYS cc_start: 0.6951 (mttt) cc_final: 0.6731 (pttp) REVERT: A 357 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5887 (ttt) REVERT: A 467 ASN cc_start: 0.1486 (OUTLIER) cc_final: 0.1027 (p0) REVERT: A 531 MET cc_start: 0.2041 (mmt) cc_final: 0.1686 (tpp) REVERT: A 552 TYR cc_start: 0.5106 (p90) cc_final: 0.3478 (p90) REVERT: A 704 MET cc_start: 0.3270 (tpp) cc_final: 0.2572 (mmp) REVERT: A 705 ASN cc_start: 0.6873 (t0) cc_final: 0.6515 (p0) REVERT: B 647 MET cc_start: 0.7341 (mmm) cc_final: 0.7098 (tpp) REVERT: B 789 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7356 (mm110) REVERT: B 883 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 930 MET cc_start: 0.7572 (mpt) cc_final: 0.7344 (mmm) REVERT: C 79 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.5868 (m-80) REVERT: C 93 LYS cc_start: 0.7529 (mmpt) cc_final: 0.7288 (tppt) REVERT: D 21 MET cc_start: 0.3732 (tpp) cc_final: 0.2028 (mtm) REVERT: D 167 LEU cc_start: 0.6458 (tt) cc_final: 0.5850 (mt) REVERT: D 169 LYS cc_start: 0.5398 (mttt) cc_final: 0.4868 (mttt) REVERT: D 396 MET cc_start: 0.3933 (mmt) cc_final: 0.3027 (tpt) REVERT: D 519 MET cc_start: -0.2906 (mtt) cc_final: -0.3208 (mtm) REVERT: D 647 MET cc_start: 0.2416 (tpt) cc_final: 0.2098 (tpt) REVERT: D 848 ASN cc_start: 0.5329 (m-40) cc_final: 0.5090 (t0) REVERT: D 913 MET cc_start: 0.2541 (mmm) cc_final: 0.1915 (mmt) REVERT: E 519 MET cc_start: 0.6601 (mmp) cc_final: 0.6273 (mmt) REVERT: E 920 TYR cc_start: 0.7103 (t80) cc_final: 0.6850 (t80) REVERT: E 925 ILE cc_start: 0.3459 (OUTLIER) cc_final: 0.2678 (tt) REVERT: E 930 MET cc_start: 0.2435 (mtt) cc_final: 0.2204 (mtt) REVERT: E 936 MET cc_start: 0.1224 (mpt) cc_final: 0.0657 (mpt) outliers start: 80 outliers final: 30 residues processed: 356 average time/residue: 0.4306 time to fit residues: 252.1063 Evaluate side-chains 260 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 423 LYS Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 781 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 871 ILE Chi-restraints excluded: chain E residue 925 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 281 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 10 optimal weight: 0.0070 chunk 249 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 363 optimal weight: 4.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 224 ASN A 483 GLN A 606 HIS A 614 ASN A 702 ASN A 829 GLN A 863 ASN B 351 ASN ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN E 467 ASN E 810 HIS ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.122554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.108389 restraints weight = 172353.218| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 3.46 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.5369 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 : 0.600 10.019 46282 Z= 0.320 Chirality : 0.043 0.222 4944 Planarity : 0.003 0.039 5890 Dihedral : 5.714 44.393 4426 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.76 % Favored : 93.02 % Rotamer: Outliers : 1.67 % Allowed : 11.22 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 3982 helix: -0.16 (0.10), residues: 2456 sheet: -4.08 (0.38), residues: 68 loop : -2.69 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 59 HIS 0.007 0.001 HIS D 658 PHE 0.031 0.002 PHE D 381 TYR 0.025 0.001 TYR E 755 ARG 0.007 0.001 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1560) hydrogen bonds : angle 4.53579 ( 4584) covalent geometry : bond 0.00290 (34350) covalent geometry : angle 0.59989 (46282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5640 (mmp) REVERT: A 453 ASP cc_start: 0.5400 (t0) cc_final: 0.5194 (t0) REVERT: A 467 ASN cc_start: 0.1348 (OUTLIER) cc_final: 0.1014 (p0) REVERT: A 520 THR cc_start: 0.1195 (OUTLIER) cc_final: -0.0177 (m) REVERT: A 552 TYR cc_start: 0.5120 (OUTLIER) cc_final: 0.3017 (p90) REVERT: A 704 MET cc_start: 0.3351 (tpp) cc_final: 0.2802 (mmp) REVERT: A 705 ASN cc_start: 0.6734 (t0) cc_final: 0.6390 (t0) REVERT: B 789 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7470 (mm110) REVERT: B 933 PHE cc_start: 0.6538 (m-80) cc_final: 0.6328 (m-80) REVERT: C 79 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: D 167 LEU cc_start: 0.6531 (tt) cc_final: 0.5846 (mt) REVERT: D 396 MET cc_start: 0.4061 (mmt) cc_final: 0.3445 (tpt) REVERT: D 565 VAL cc_start: 0.5268 (OUTLIER) cc_final: 0.5065 (t) REVERT: D 913 MET cc_start: 0.2569 (mmm) cc_final: 0.2184 (mmt) REVERT: E 519 MET cc_start: 0.6826 (mmp) cc_final: 0.6417 (mmt) REVERT: E 531 MET cc_start: 0.8496 (mmm) cc_final: 0.8290 (mmt) REVERT: E 930 MET cc_start: 0.2387 (mtt) cc_final: 0.2182 (mtm) REVERT: E 936 MET cc_start: 0.1015 (mpt) cc_final: 0.0519 (mpt) outliers start: 62 outliers final: 25 residues processed: 298 average time/residue: 0.4556 time to fit residues: 224.0321 Evaluate side-chains 245 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 951 TYR Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 666 ASN Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 871 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 23 PHE Chi-restraints excluded: chain F residue 51 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 346 optimal weight: 6.9990 chunk 202 optimal weight: 0.5980 chunk 373 optimal weight: 0.5980 chunk 246 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 24 optimal weight: 50.0000 chunk 333 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN B 171 HIS B 609 HIS ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 927 ASN E 939 GLN E 973 ASN E 992 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.121361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.104291 restraints weight = 162239.128| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 4.80 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.6564 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= 0.184 Angle : 0.667 10.677 46282 Z= 0.356 Chirality : 0.045 0.210 4944 Planarity : 0.004 0.085 5890 Dihedral : 5.705 43.912 4426 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.61 % Favored : 91.21 % Rotamer: Outliers : 2.21 % Allowed : 12.06 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3982 helix: -0.05 (0.10), residues: 2396 sheet: -4.33 (0.37), residues: 80 loop : -2.57 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 25 HIS 0.010 0.001 HIS A 118 PHE 0.035 0.002 PHE D 811 TYR 0.037 0.002 TYR A 479 ARG 0.012 0.001 ARG D 613 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 1560) hydrogen bonds : angle 4.71588 ( 4584) covalent geometry : bond 0.00412 (34350) covalent geometry : angle 0.66725 (46282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 261 time to evaluate : 3.691 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: A 184 VAL cc_start: 0.6236 (t) cc_final: 0.5839 (p) REVERT: A 357 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6553 (ttt) REVERT: A 382 ASN cc_start: 0.7343 (m-40) cc_final: 0.7064 (t0) REVERT: A 385 PHE cc_start: 0.6219 (OUTLIER) cc_final: 0.5959 (t80) REVERT: A 389 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7497 (mt-10) REVERT: A 421 MET cc_start: 0.7609 (ttm) cc_final: 0.7386 (mtp) REVERT: A 467 ASN cc_start: 0.2424 (OUTLIER) cc_final: 0.2005 (p0) REVERT: A 552 TYR cc_start: 0.5429 (OUTLIER) cc_final: 0.3038 (p90) REVERT: A 704 MET cc_start: 0.4473 (tpp) cc_final: 0.4129 (mmm) REVERT: A 705 ASN cc_start: 0.6614 (t0) cc_final: 0.6359 (t0) REVERT: B 107 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8191 (t80) REVERT: B 647 MET cc_start: 0.7521 (tpp) cc_final: 0.7302 (tpp) REVERT: B 789 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7635 (mm110) REVERT: B 883 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8199 (mm-30) REVERT: B 922 LEU cc_start: 0.8923 (mm) cc_final: 0.8711 (tt) REVERT: B 933 PHE cc_start: 0.7365 (m-80) cc_final: 0.6516 (m-80) REVERT: B 940 TYR cc_start: 0.7328 (t80) cc_final: 0.7091 (t80) REVERT: D 167 LEU cc_start: 0.7281 (tt) cc_final: 0.6245 (mt) REVERT: D 385 PHE cc_start: 0.4770 (OUTLIER) cc_final: 0.4310 (m-10) REVERT: D 519 MET cc_start: -0.3046 (mtm) cc_final: -0.3553 (mtm) REVERT: D 565 VAL cc_start: 0.4776 (OUTLIER) cc_final: 0.4560 (t) REVERT: D 590 ASP cc_start: 0.1775 (t0) cc_final: 0.1560 (t70) REVERT: D 711 GLN cc_start: -0.0462 (pt0) cc_final: -0.1221 (mt0) REVERT: D 815 PHE cc_start: 0.4809 (t80) cc_final: 0.4482 (t80) REVERT: D 913 MET cc_start: 0.2660 (mmm) cc_final: 0.2315 (mmt) REVERT: E 920 TYR cc_start: 0.7329 (t80) cc_final: 0.7126 (t80) REVERT: E 936 MET cc_start: 0.0861 (mpt) cc_final: 0.0515 (mpt) REVERT: F 43 TYR cc_start: 0.5574 (p90) cc_final: 0.5275 (p90) REVERT: F 81 PHE cc_start: 0.5857 (t80) cc_final: 0.5617 (t80) outliers start: 82 outliers final: 32 residues processed: 322 average time/residue: 0.4405 time to fit residues: 233.8147 Evaluate side-chains 265 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 1001 MET Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 871 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 51 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 34 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 385 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 345 optimal weight: 7.9990 chunk 368 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 195 GLN ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN D 332 HIS D 415 HIS ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 927 ASN E 67 HIS E 93 ASN E 351 ASN E 467 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 927 ASN ** 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 = 0.4615 r_free = 0.4615 target = 0.119700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.102577 restraints weight = 161843.827| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 4.50 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.7440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34350 Z= 0.184 Angle : 0.658 11.343 46282 Z= 0.350 Chirality : 0.045 0.219 4944 Planarity : 0.004 0.053 5890 Dihedral : 5.678 44.957 4426 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.81 % Favored : 92.06 % Rotamer: Outliers : 2.21 % Allowed : 13.21 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3982 helix: -0.05 (0.10), residues: 2396 sheet: -3.73 (0.38), residues: 104 loop : -2.50 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 448 HIS 0.009 0.001 HIS A 118 PHE 0.026 0.002 PHE D 699 TYR 0.026 0.002 TYR A 479 ARG 0.005 0.001 ARG D 145 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 1560) hydrogen bonds : angle 4.76148 ( 4584) covalent geometry : bond 0.00413 (34350) covalent geometry : angle 0.65777 (46282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 252 time to evaluate : 3.593 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 382 ASN cc_start: 0.7450 (m-40) cc_final: 0.7105 (t0) REVERT: A 385 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.4764 (t80) REVERT: A 389 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7475 (mt-10) REVERT: A 467 ASN cc_start: 0.1909 (OUTLIER) cc_final: 0.1669 (p0) REVERT: A 550 PHE cc_start: 0.2735 (OUTLIER) cc_final: 0.1145 (t80) REVERT: A 552 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.2329 (p90) REVERT: B 107 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8199 (t80) REVERT: B 789 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7711 (mm110) REVERT: C 79 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: C 93 LYS cc_start: 0.7862 (mttt) cc_final: 0.7580 (mtpt) REVERT: D 295 GLU cc_start: 0.4024 (OUTLIER) cc_final: 0.3573 (pt0) REVERT: D 357 MET cc_start: 0.5467 (tpp) cc_final: 0.5031 (tpt) REVERT: D 385 PHE cc_start: 0.4867 (OUTLIER) cc_final: 0.4251 (m-10) REVERT: D 552 TYR cc_start: 0.4198 (OUTLIER) cc_final: 0.2114 (p90) REVERT: D 569 MET cc_start: 0.7964 (ppp) cc_final: 0.7213 (ppp) REVERT: D 711 GLN cc_start: -0.0477 (pt0) cc_final: -0.1009 (mt0) REVERT: D 827 LEU cc_start: -0.1678 (pt) cc_final: -0.2448 (tp) REVERT: D 913 MET cc_start: 0.2726 (mmm) cc_final: 0.2441 (mmt) REVERT: E 7 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7842 (tp30) REVERT: E 829 GLN cc_start: 0.7812 (pp30) cc_final: 0.7111 (tp40) REVERT: E 920 TYR cc_start: 0.7353 (t80) cc_final: 0.7008 (t80) REVERT: E 925 ILE cc_start: 0.3969 (OUTLIER) cc_final: 0.3054 (tt) REVERT: E 930 MET cc_start: 0.3158 (mtm) cc_final: 0.2920 (mtm) REVERT: E 936 MET cc_start: 0.0908 (mpt) cc_final: 0.0662 (mpt) REVERT: E 976 MET cc_start: 0.4418 (mtt) cc_final: 0.4211 (mmm) REVERT: F 81 PHE cc_start: 0.6027 (t80) cc_final: 0.5798 (t80) REVERT: F 114 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7428 (mtpt) outliers start: 82 outliers final: 36 residues processed: 311 average time/residue: 0.4567 time to fit residues: 230.8189 Evaluate side-chains 264 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 1001 MET Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 925 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 114 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 297 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 282 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 198 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 351 ASN A 467 ASN A 477 ASN A 614 ASN A 711 GLN ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 HIS ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 ASN D 992 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.117528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.100944 restraints weight = 161378.228| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 4.56 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.8338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 34350 Z= 0.211 Angle : 0.708 13.240 46282 Z= 0.372 Chirality : 0.046 0.251 4944 Planarity : 0.004 0.059 5890 Dihedral : 5.784 45.885 4426 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.29 % Favored : 90.61 % Rotamer: Outliers : 2.40 % Allowed : 14.05 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.13), residues: 3982 helix: -0.16 (0.10), residues: 2412 sheet: -4.02 (0.36), residues: 108 loop : -2.49 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 143 HIS 0.009 0.001 HIS A 118 PHE 0.033 0.002 PHE D 699 TYR 0.040 0.002 TYR A 479 ARG 0.006 0.001 ARG F 72 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 1560) hydrogen bonds : angle 4.93171 ( 4584) covalent geometry : bond 0.00479 (34350) covalent geometry : angle 0.70800 (46282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 237 time to evaluate : 3.582 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 382 ASN cc_start: 0.7639 (m-40) cc_final: 0.7374 (m110) REVERT: A 385 PHE cc_start: 0.6475 (OUTLIER) cc_final: 0.4919 (t80) REVERT: A 396 MET cc_start: 0.8123 (tpp) cc_final: 0.7275 (tpp) REVERT: A 527 LEU cc_start: 0.5005 (tp) cc_final: 0.4537 (pt) REVERT: A 550 PHE cc_start: 0.2989 (OUTLIER) cc_final: 0.0923 (t80) REVERT: A 552 TYR cc_start: 0.4912 (OUTLIER) cc_final: 0.2356 (p90) REVERT: A 578 MET cc_start: 0.5569 (tpp) cc_final: 0.5357 (tpp) REVERT: A 713 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8270 (tp) REVERT: A 769 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7917 (tppt) REVERT: A 813 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7746 (tptt) REVERT: B 107 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8186 (t80) REVERT: B 789 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7581 (mm-40) REVERT: B 883 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8199 (mm-30) REVERT: C 79 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: D 251 SER cc_start: 0.3527 (OUTLIER) cc_final: 0.3194 (m) REVERT: D 295 GLU cc_start: 0.3933 (OUTLIER) cc_final: 0.3614 (pt0) REVERT: D 357 MET cc_start: 0.5759 (tpp) cc_final: 0.5335 (tpt) REVERT: D 385 PHE cc_start: 0.4628 (OUTLIER) cc_final: 0.4279 (m-10) REVERT: D 426 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.4960 (mp0) REVERT: D 552 TYR cc_start: 0.4260 (OUTLIER) cc_final: 0.2028 (p90) REVERT: D 569 MET cc_start: 0.7942 (ppp) cc_final: 0.7215 (ppp) REVERT: D 647 MET cc_start: 0.7103 (ttm) cc_final: 0.6175 (mtp) REVERT: D 815 PHE cc_start: 0.5020 (t80) cc_final: 0.4725 (t80) REVERT: D 827 LEU cc_start: -0.1037 (pt) cc_final: -0.1711 (tp) REVERT: D 913 MET cc_start: 0.2918 (mmm) cc_final: 0.2468 (mmt) REVERT: D 960 LYS cc_start: 0.3790 (mttt) cc_final: 0.3122 (mttt) REVERT: E 829 GLN cc_start: 0.7705 (pp30) cc_final: 0.7071 (tp40) REVERT: E 839 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: E 920 TYR cc_start: 0.7296 (t80) cc_final: 0.7084 (t80) REVERT: E 936 MET cc_start: 0.0973 (mpt) cc_final: 0.0700 (mpt) REVERT: E 976 MET cc_start: 0.4552 (mtt) cc_final: 0.4248 (mmm) REVERT: F 114 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7544 (mtpt) outliers start: 89 outliers final: 44 residues processed: 305 average time/residue: 0.4608 time to fit residues: 234.4797 Evaluate side-chains 271 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 951 TYR Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 666 ASN Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 835 ILE Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 973 ASN Chi-restraints excluded: chain D residue 1001 MET Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 839 PHE Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 51 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 72 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 chunk 358 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 chunk 24 optimal weight: 30.0000 chunk 235 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 711 GLN A 863 ASN B 666 ASN B 711 GLN D 711 GLN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.118719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.102256 restraints weight = 160247.847| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 4.45 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.8498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34350 Z= 0.129 Angle : 0.625 14.550 46282 Z= 0.327 Chirality : 0.043 0.300 4944 Planarity : 0.003 0.055 5890 Dihedral : 5.469 41.716 4426 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.79 % Rotamer: Outliers : 1.83 % Allowed : 14.97 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3982 helix: 0.13 (0.11), residues: 2424 sheet: -3.71 (0.40), residues: 96 loop : -2.39 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 601 HIS 0.016 0.001 HIS A 979 PHE 0.023 0.001 PHE D 699 TYR 0.039 0.001 TYR A 479 ARG 0.006 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 1560) hydrogen bonds : angle 4.60178 ( 4584) covalent geometry : bond 0.00283 (34350) covalent geometry : angle 0.62486 (46282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 221 time to evaluate : 3.483 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 385 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.5717 (t80) REVERT: A 396 MET cc_start: 0.8004 (tpp) cc_final: 0.7501 (tpp) REVERT: A 527 LEU cc_start: 0.5353 (tp) cc_final: 0.4936 (tp) REVERT: A 550 PHE cc_start: 0.2392 (OUTLIER) cc_final: 0.0879 (t80) REVERT: A 552 TYR cc_start: 0.4618 (OUTLIER) cc_final: 0.2265 (p90) REVERT: A 713 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8101 (tp) REVERT: A 769 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7929 (tppt) REVERT: B 107 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8133 (t80) REVERT: B 802 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7320 (ptm160) REVERT: B 955 ILE cc_start: 0.6075 (mt) cc_final: 0.5764 (mm) REVERT: C 79 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: D 85 LEU cc_start: 0.4301 (OUTLIER) cc_final: 0.3037 (tp) REVERT: D 385 PHE cc_start: 0.4081 (OUTLIER) cc_final: 0.3843 (m-10) REVERT: D 552 TYR cc_start: 0.4122 (OUTLIER) cc_final: 0.2145 (p90) REVERT: D 578 MET cc_start: 0.3372 (mmp) cc_final: 0.2894 (mmm) REVERT: D 647 MET cc_start: 0.7007 (ttm) cc_final: 0.6329 (mtp) REVERT: D 827 LEU cc_start: -0.0972 (pt) cc_final: -0.1665 (tp) REVERT: E 829 GLN cc_start: 0.7721 (pp30) cc_final: 0.7167 (tp40) REVERT: E 920 TYR cc_start: 0.7196 (t80) cc_final: 0.6517 (t80) REVERT: E 925 ILE cc_start: 0.3967 (OUTLIER) cc_final: 0.3149 (tt) REVERT: E 930 MET cc_start: 0.3527 (mtm) cc_final: 0.2898 (ptp) REVERT: E 994 LYS cc_start: 0.7259 (mttm) cc_final: 0.7004 (mptt) REVERT: F 43 TYR cc_start: 0.5405 (OUTLIER) cc_final: 0.5149 (p90) REVERT: F 98 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7767 (mp) REVERT: F 114 LYS cc_start: 0.7703 (mtpt) cc_final: 0.7469 (mtmt) outliers start: 68 outliers final: 32 residues processed: 274 average time/residue: 0.4216 time to fit residues: 192.5345 Evaluate side-chains 250 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 395 CYS Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 936 MET Chi-restraints excluded: chain D residue 973 ASN Chi-restraints excluded: chain D residue 1001 MET Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 925 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 43 TYR Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 98 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 48 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 349 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 307 optimal weight: 5.9990 chunk 396 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 654 ASN D 658 HIS D 666 ASN E 93 ASN E 351 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.116323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.099476 restraints weight = 158841.309| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 4.44 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.9064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 34350 Z= 0.197 Angle : 0.702 13.041 46282 Z= 0.368 Chirality : 0.046 0.318 4944 Planarity : 0.004 0.058 5890 Dihedral : 5.657 42.981 4426 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.24 % Favored : 90.71 % Rotamer: Outliers : 1.56 % Allowed : 15.51 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3982 helix: 0.01 (0.11), residues: 2422 sheet: -3.65 (0.40), residues: 98 loop : -2.48 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 25 HIS 0.016 0.002 HIS A 881 PHE 0.033 0.002 PHE D 699 TYR 0.052 0.002 TYR A 479 ARG 0.006 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 1560) hydrogen bonds : angle 4.86581 ( 4584) covalent geometry : bond 0.00450 (34350) covalent geometry : angle 0.70171 (46282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 227 time to evaluate : 4.197 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 98 MET cc_start: 0.8063 (mpp) cc_final: 0.7378 (ttm) REVERT: A 149 PHE cc_start: 0.1660 (OUTLIER) cc_final: 0.1316 (m-10) REVERT: A 169 LYS cc_start: 0.4700 (mttt) cc_final: 0.4209 (mttt) REVERT: A 357 MET cc_start: 0.6706 (ttt) cc_final: 0.5939 (tpp) REVERT: A 399 ASP cc_start: 0.6199 (t70) cc_final: 0.5990 (t70) REVERT: A 527 LEU cc_start: 0.5539 (tp) cc_final: 0.5035 (pt) REVERT: A 550 PHE cc_start: 0.3169 (OUTLIER) cc_final: 0.0757 (t80) REVERT: A 552 TYR cc_start: 0.4823 (OUTLIER) cc_final: 0.2363 (p90) REVERT: A 713 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8314 (tp) REVERT: A 769 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8098 (tppt) REVERT: B 107 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8158 (t80) REVERT: B 955 ILE cc_start: 0.6311 (mt) cc_final: 0.6044 (mm) REVERT: C 79 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: D 85 LEU cc_start: 0.4472 (mt) cc_final: 0.4046 (tt) REVERT: D 385 PHE cc_start: 0.4673 (OUTLIER) cc_final: 0.4340 (m-10) REVERT: D 434 ASP cc_start: 0.4778 (OUTLIER) cc_final: 0.4400 (m-30) REVERT: D 519 MET cc_start: -0.3929 (mtm) cc_final: -0.4612 (mtm) REVERT: D 552 TYR cc_start: 0.4257 (OUTLIER) cc_final: 0.2132 (p90) REVERT: D 647 MET cc_start: 0.7284 (ttm) cc_final: 0.6626 (mtp) REVERT: D 815 PHE cc_start: 0.5292 (t80) cc_final: 0.4966 (t80) REVERT: D 827 LEU cc_start: -0.0327 (pt) cc_final: -0.0937 (tp) REVERT: D 960 LYS cc_start: 0.4342 (mttt) cc_final: 0.3513 (mttt) REVERT: E 829 GLN cc_start: 0.7769 (pp30) cc_final: 0.7197 (tp40) REVERT: E 919 TRP cc_start: 0.5127 (m-10) cc_final: 0.4863 (m-10) REVERT: E 920 TYR cc_start: 0.7394 (t80) cc_final: 0.6710 (t80) REVERT: E 930 MET cc_start: 0.3764 (mtm) cc_final: 0.3080 (ptp) REVERT: F 23 PHE cc_start: 0.7362 (m-10) cc_final: 0.7103 (m-10) REVERT: F 43 TYR cc_start: 0.5691 (OUTLIER) cc_final: 0.5272 (p90) REVERT: F 98 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7642 (mp) REVERT: F 114 LYS cc_start: 0.7911 (mtpt) cc_final: 0.7635 (mtpt) outliers start: 58 outliers final: 31 residues processed: 272 average time/residue: 0.4374 time to fit residues: 200.7611 Evaluate side-chains 247 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 666 ASN Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain D residue 973 ASN Chi-restraints excluded: chain D residue 1001 MET Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 43 TYR Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 276 optimal weight: 10.0000 chunk 259 optimal weight: 0.9980 chunk 181 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 397 optimal weight: 9.9990 chunk 270 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 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 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.116210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.099740 restraints weight = 158770.432| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 4.26 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.9392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34350 Z= 0.171 Angle : 0.676 13.982 46282 Z= 0.353 Chirality : 0.045 0.343 4944 Planarity : 0.004 0.057 5890 Dihedral : 5.597 41.674 4426 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.31 % Favored : 91.61 % Rotamer: Outliers : 1.35 % Allowed : 15.75 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3982 helix: 0.07 (0.11), residues: 2429 sheet: -3.78 (0.43), residues: 91 loop : -2.43 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 757 HIS 0.006 0.001 HIS A 881 PHE 0.031 0.002 PHE B 942 TYR 0.042 0.002 TYR A 479 ARG 0.007 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 1560) hydrogen bonds : angle 4.80761 ( 4584) covalent geometry : bond 0.00385 (34350) covalent geometry : angle 0.67601 (46282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7964 Ramachandran restraints generated. 3982 Oldfield, 0 Emsley, 3982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 212 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7946 (mpp) cc_final: 0.7362 (ttm) REVERT: A 149 PHE cc_start: 0.1715 (OUTLIER) cc_final: 0.1340 (m-10) REVERT: A 169 LYS cc_start: 0.4634 (mttt) cc_final: 0.4060 (mttp) REVERT: A 357 MET cc_start: 0.6679 (ttt) cc_final: 0.6078 (tpt) REVERT: A 399 ASP cc_start: 0.6161 (t70) cc_final: 0.5907 (t70) REVERT: A 527 LEU cc_start: 0.5965 (tp) cc_final: 0.5382 (pt) REVERT: A 550 PHE cc_start: 0.2938 (OUTLIER) cc_final: 0.0528 (t80) REVERT: A 552 TYR cc_start: 0.4688 (OUTLIER) cc_final: 0.2197 (p90) REVERT: A 713 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8205 (tp) REVERT: A 769 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8145 (tppt) REVERT: B 107 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8216 (t80) REVERT: B 290 MET cc_start: 0.7657 (mmm) cc_final: 0.7362 (mmm) REVERT: B 955 ILE cc_start: 0.6008 (mt) cc_final: 0.5804 (mm) REVERT: C 79 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: D 311 TYR cc_start: 0.3247 (t80) cc_final: 0.2972 (t80) REVERT: D 385 PHE cc_start: 0.4551 (OUTLIER) cc_final: 0.4254 (m-10) REVERT: D 421 MET cc_start: 0.1702 (OUTLIER) cc_final: 0.1489 (ttt) REVERT: D 434 ASP cc_start: 0.4704 (OUTLIER) cc_final: 0.4353 (m-30) REVERT: D 552 TYR cc_start: 0.4105 (OUTLIER) cc_final: 0.2077 (p90) REVERT: D 578 MET cc_start: 0.3580 (mmp) cc_final: 0.3114 (mmm) REVERT: D 647 MET cc_start: 0.7298 (ttm) cc_final: 0.6572 (mtp) REVERT: D 661 ILE cc_start: 0.4271 (mp) cc_final: 0.4041 (tt) REVERT: D 774 ILE cc_start: 0.6108 (mt) cc_final: 0.5829 (mm) REVERT: D 815 PHE cc_start: 0.5371 (t80) cc_final: 0.5064 (t80) REVERT: D 827 LEU cc_start: -0.0419 (pt) cc_final: -0.0787 (tt) REVERT: E 274 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8644 (mp) REVERT: E 829 GLN cc_start: 0.7681 (pp30) cc_final: 0.7161 (tp-100) REVERT: E 866 MET cc_start: 0.1921 (mmt) cc_final: 0.1527 (mmt) REVERT: E 920 TYR cc_start: 0.7327 (t80) cc_final: 0.6783 (t80) REVERT: E 930 MET cc_start: 0.3958 (mtm) cc_final: 0.3514 (ptp) REVERT: E 936 MET cc_start: -0.0619 (mpt) cc_final: -0.1060 (mpp) REVERT: F 23 PHE cc_start: 0.7190 (m-10) cc_final: 0.6943 (m-10) REVERT: F 98 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7754 (mp) REVERT: F 114 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7669 (mtpt) outliers start: 50 outliers final: 33 residues processed: 255 average time/residue: 0.4367 time to fit residues: 187.7118 Evaluate side-chains 247 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 201 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 666 ASN Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain D residue 973 ASN Chi-restraints excluded: chain D residue 1001 MET Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 859 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 361 optimal weight: 8.9990 chunk 358 optimal weight: 0.9980 chunk 346 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 235 optimal weight: 0.3980 chunk 362 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 347 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 HIS D 666 ASN ** E 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 927 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.117144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.100549 restraints weight = 159966.501| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 4.50 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.9495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34350 Z= 0.126 Angle : 0.645 13.266 46282 Z= 0.333 Chirality : 0.043 0.293 4944 Planarity : 0.003 0.054 5890 Dihedral : 5.376 41.622 4426 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.16 % Favored : 91.81 % Rotamer: Outliers : 1.27 % Allowed : 15.91 % Favored : 82.82 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 3982 helix: 0.28 (0.11), residues: 2434 sheet: -3.38 (0.45), residues: 98 loop : -2.37 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 60 HIS 0.006 0.001 HIS A 978 PHE 0.045 0.002 PHE F 81 TYR 0.037 0.002 TYR A 479 ARG 0.007 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 1560) hydrogen bonds : angle 4.59659 ( 4584) covalent geometry : bond 0.00278 (34350) covalent geometry : angle 0.64474 (46282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13574.06 seconds wall clock time: 237 minutes 55.82 seconds (14275.82 seconds total)