Starting phenix.real_space_refine on Tue Mar 19 10:20:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjj_40091/03_2024/8gjj_40091.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjj_40091/03_2024/8gjj_40091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjj_40091/03_2024/8gjj_40091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjj_40091/03_2024/8gjj_40091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjj_40091/03_2024/8gjj_40091.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gjj_40091/03_2024/8gjj_40091.pdb" } resolution = 3.08 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= 0.001 sd= 0.027 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 84 5.16 5 C 15521 2.51 5 N 3860 2.21 5 O 4463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23928 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7976 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 7982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7982 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Chain: "C" Number of atoms: 7970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7970 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 12.40, per 1000 atoms: 0.52 Number of scatterers: 23928 At special positions: 0 Unit cell: (118.77, 121.98, 146.59, 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 84 16.00 O 4463 8.00 N 3860 7.00 C 15521 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 - 3.50 Amino acid : False - 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: 9.15 Conformation dependent library (CDL) restraints added in 4.2 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 24 sheets defined 60.4% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'B' and resid 1 through 8 removed outlier: 3.743A pdb=" N PHE B 6 " --> pdb=" O PHE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.300A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.579A pdb=" N GLU B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 263 through 266 No H-bonds generated for 'chain 'B' and resid 263 through 266' Processing helix chain 'B' and resid 299 through 316 Processing helix chain 'B' and resid 330 through 360 removed outlier: 3.975A pdb=" N VAL B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 388 removed outlier: 3.571A pdb=" N THR B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) Proline residue: B 369 - end of helix Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 392 through 424 removed outlier: 4.443A pdb=" N GLY B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 459 removed outlier: 5.642A pdb=" N SER B 442 " --> pdb=" O ASN B 438 " (cutoff:3.500A) Proline residue: B 443 - end of helix Proline residue: B 457 - end of helix Processing helix chain 'B' and resid 463 through 498 removed outlier: 4.089A pdb=" N ILE B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 507 through 534 Processing helix chain 'B' and resid 534 through 556 removed outlier: 4.211A pdb=" N PHE B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 598 removed outlier: 3.511A pdb=" N THR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET B 598 " --> pdb=" O ASN B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 649 Processing helix chain 'B' and resid 685 through 703 Processing helix chain 'B' and resid 725 through 732 Processing helix chain 'B' and resid 735 through 747 Processing helix chain 'B' and resid 770 through 773 removed outlier: 3.682A pdb=" N ARG B 773 " --> pdb=" O GLY B 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 770 through 773' Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.183A pdb=" N ASN B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 777 through 782' Processing helix chain 'B' and resid 829 through 845 Processing helix chain 'B' and resid 855 through 863 Processing helix chain 'B' and resid 867 through 887 Processing helix chain 'B' and resid 891 through 898 removed outlier: 4.192A pdb=" N VAL B 895 " --> pdb=" O MET B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 914 removed outlier: 4.020A pdb=" N VAL B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 950 Processing helix chain 'B' and resid 953 through 985 removed outlier: 4.541A pdb=" N ARG B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Proline residue: B 968 - end of helix Proline residue: B 982 - end of helix removed outlier: 3.902A pdb=" N PHE B 985 " --> pdb=" O LEU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1011 Processing helix chain 'B' and resid 1011 through 1032 Proline residue: B1017 - end of helix Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.691A pdb=" N PHE A 6 " --> pdb=" O PHE A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 54 through 71 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.605A pdb=" N ALA A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.503A pdb=" N LYS A 123 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 removed outlier: 4.459A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 263 through 266 No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 299 through 316 Processing helix chain 'A' and resid 330 through 361 Processing helix chain 'A' and resid 362 through 371 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.548A pdb=" N VAL A 375 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 4.662A pdb=" N GLY A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 455 removed outlier: 5.579A pdb=" N SER A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 455 through 461 removed outlier: 3.930A pdb=" N SER A 459 " --> pdb=" O PHE A 455 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 499 removed outlier: 3.826A pdb=" N THR A 475 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 507 through 534 Processing helix chain 'A' and resid 535 through 556 Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.571A pdb=" N GLN A 597 " --> pdb=" O LYS A 593 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 598 " --> pdb=" O ASN A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 685 through 702 removed outlier: 3.817A pdb=" N GLN A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 735 through 747 Processing helix chain 'A' and resid 777 through 782 Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 829 through 846 removed outlier: 3.650A pdb=" N GLY A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 864 removed outlier: 3.596A pdb=" N TYR A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 887 Processing helix chain 'A' and resid 889 through 897 removed outlier: 3.936A pdb=" N LEU A 893 " --> pdb=" O TRP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 913 removed outlier: 3.687A pdb=" N ALA A 902 " --> pdb=" O ALA A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 950 removed outlier: 3.715A pdb=" N GLY A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 939 " --> pdb=" O ASN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 985 removed outlier: 4.849A pdb=" N ARG A 967 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Proline residue: A 968 - end of helix Proline residue: A 982 - end of helix Processing helix chain 'A' and resid 990 through 1011 removed outlier: 4.067A pdb=" N GLY A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1032 Proline residue: A1017 - end of helix Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.725A pdb=" N PHE C 6 " --> pdb=" O PHE C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 31 Processing helix chain 'C' and resid 54 through 62 Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.528A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.668A pdb=" N GLU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 200 through 212 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 263 through 266 No H-bonds generated for 'chain 'C' and resid 263 through 266' Processing helix chain 'C' and resid 299 through 317 removed outlier: 3.803A pdb=" N ASN C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 360 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 366 through 388 removed outlier: 3.616A pdb=" N MET C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 392 through 424 removed outlier: 4.016A pdb=" N GLY C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 460 removed outlier: 5.078A pdb=" N SER C 442 " --> pdb=" O ASN C 438 " (cutoff:3.500A) Proline residue: C 443 - end of helix Proline residue: C 457 - end of helix removed outlier: 3.579A pdb=" N PHE C 460 " --> pdb=" O ILE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 499 removed outlier: 3.544A pdb=" N GLY C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR C 491 " --> pdb=" O ALA C 487 " (cutoff:3.500A) Proline residue: C 492 - end of helix Processing helix chain 'C' and resid 507 through 534 Processing helix chain 'C' and resid 534 through 556 removed outlier: 3.899A pdb=" N PHE C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 598 removed outlier: 3.685A pdb=" N THR C 584 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 597 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET C 598 " --> pdb=" O ASN C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 649 Processing helix chain 'C' and resid 685 through 703 removed outlier: 3.725A pdb=" N THR C 702 " --> pdb=" O GLU C 698 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 732 Processing helix chain 'C' and resid 735 through 747 Processing helix chain 'C' and resid 770 through 773 removed outlier: 3.634A pdb=" N ARG C 773 " --> pdb=" O GLY C 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 770 through 773' Processing helix chain 'C' and resid 775 through 781 removed outlier: 4.421A pdb=" N LEU C 779 " --> pdb=" O GLN C 776 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 781 " --> pdb=" O ALA C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 845 Processing helix chain 'C' and resid 855 through 887 removed outlier: 4.214A pdb=" N LYS C 864 " --> pdb=" O GLU C 860 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY C 865 " --> pdb=" O VAL C 861 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA C 866 " --> pdb=" O SER C 862 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY C 867 " --> pdb=" O SER C 863 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA C 868 " --> pdb=" O LYS C 864 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR C 869 " --> pdb=" O GLY C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 899 removed outlier: 4.206A pdb=" N VAL C 895 " --> pdb=" O MET C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 914 removed outlier: 4.059A pdb=" N VAL C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 949 Processing helix chain 'C' and resid 953 through 985 removed outlier: 4.383A pdb=" N ARG C 967 " --> pdb=" O LYS C 963 " (cutoff:3.500A) Proline residue: C 968 - end of helix Proline residue: C 982 - end of helix removed outlier: 4.054A pdb=" N PHE C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1032 removed outlier: 3.612A pdb=" N ARG C 994 " --> pdb=" O GLY C 990 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C1013 " --> pdb=" O SER C1009 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE C1014 " --> pdb=" O THR C1010 " (cutoff:3.500A) Proline residue: C1017 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA2, first strand: chain 'B' and resid 172 through 177 removed outlier: 6.609A pdb=" N VAL B 172 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN B 295 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 174 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 286 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 144 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 138 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 294 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE B 136 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 328 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 322 through 324 removed outlier: 7.976A pdb=" N ILE B 136 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 294 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 138 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 144 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 286 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 623 " --> pdb=" O LEU B 607 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ALA B 621 " --> pdb=" O GLY B 609 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ASP B 611 " --> pdb=" O GLU B 619 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N GLU B 619 " --> pdb=" O ASP B 611 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 572 " --> pdb=" O TYR B 658 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 267 through 273 removed outlier: 7.705A pdb=" N TYR B 183 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN B 763 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS B 760 " --> pdb=" O PRO B 756 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE B 762 " --> pdb=" O ASP B 754 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP B 754 " --> pdb=" O PHE B 762 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 764 " --> pdb=" O VAL B 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 220 removed outlier: 3.905A pdb=" N SER B 234 " --> pdb=" O PRO C 718 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 799 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 251 through 254 removed outlier: 3.610A pdb=" N ARG B 253 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 706 through 711 removed outlier: 3.504A pdb=" N ASN B 708 " --> pdb=" O ASP B 823 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 798 through 804 removed outlier: 4.138A pdb=" N SER A 234 " --> pdb=" O PRO B 718 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 783 through 785 Processing sheet with id=AB1, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.433A pdb=" N THR A 43 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 78 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS A 810 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.571A pdb=" N GLU A 138 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 294 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 136 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N LEU A 137 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP A 329 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 139 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 267 through 273 removed outlier: 8.061A pdb=" N TYR A 183 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 763 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN A 753 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE A 766 " --> pdb=" O TYR A 751 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N TYR A 751 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 251 through 254 Processing sheet with id=AB5, first strand: chain 'A' and resid 279 through 282 removed outlier: 5.911A pdb=" N ALA A 621 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASP A 611 " --> pdb=" O GLU A 619 " (cutoff:3.500A) removed outlier: 9.670A pdb=" N GLU A 619 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 706 through 711 removed outlier: 4.292A pdb=" N VAL A 709 " --> pdb=" O GLN A 821 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLN A 821 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR A 711 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 819 " --> pdb=" O THR A 711 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 822 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 798 through 805 removed outlier: 3.754A pdb=" N SER C 234 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN C 238 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE A 724 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 239 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLN C 214 " --> pdb=" O GLY C 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.590A pdb=" N TYR C 78 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.509A pdb=" N ALA C 286 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU C 294 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE C 136 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LEU C 137 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP C 329 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C 139 " --> pdb=" O PRO C 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.169A pdb=" N GLY C 280 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 267 through 273 removed outlier: 7.713A pdb=" N TYR C 183 " --> pdb=" O ASN C 761 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN C 763 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN C 753 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE C 766 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR C 751 " --> pdb=" O ILE C 766 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 251 through 254 Processing sheet with id=AC5, first strand: chain 'C' and resid 707 through 711 removed outlier: 4.872A pdb=" N ASN C 708 " --> pdb=" O ASP C 823 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 823 " --> pdb=" O ASN C 708 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY C 822 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU C 675 " --> pdb=" O SER C 854 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 783 through 785 1595 hydrogen bonds defined for protein. 4689 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: 11.58 Time building geometry restraints manager: 9.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7590 1.34 - 1.46: 3642 1.46 - 1.57: 12996 1.57 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 24390 Sorted by residual: bond pdb=" C VAL B 288 " pdb=" N PRO B 289 " ideal model delta sigma weight residual 1.335 1.318 0.017 8.70e-03 1.32e+04 3.87e+00 bond pdb=" C GLN C 242 " pdb=" N THR C 243 " ideal model delta sigma weight residual 1.327 1.273 0.054 2.86e-02 1.22e+03 3.53e+00 bond pdb=" C LYS A 228 " pdb=" N SER A 229 " ideal model delta sigma weight residual 1.331 1.293 0.038 2.07e-02 2.33e+03 3.46e+00 bond pdb=" C VAL A 288 " pdb=" N PRO A 289 " ideal model delta sigma weight residual 1.334 1.321 0.013 1.11e-02 8.12e+03 1.42e+00 bond pdb=" C PRO B 663 " pdb=" N PRO B 664 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.19e-02 7.06e+03 1.36e+00 ... (remaining 24385 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.86: 517 105.86 - 112.92: 13470 112.92 - 119.98: 8067 119.98 - 127.05: 10909 127.05 - 134.11: 169 Bond angle restraints: 33132 Sorted by residual: angle pdb=" C LEU A 360 " pdb=" N LYS A 361 " pdb=" CA LYS A 361 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 9.99e+00 angle pdb=" CA VAL A 561 " pdb=" C VAL A 561 " pdb=" N PRO A 562 " ideal model delta sigma weight residual 116.57 119.35 -2.78 9.80e-01 1.04e+00 8.04e+00 angle pdb=" C SER B 459 " pdb=" N PHE B 460 " pdb=" CA PHE B 460 " ideal model delta sigma weight residual 122.61 127.00 -4.39 1.56e+00 4.11e-01 7.91e+00 angle pdb=" C VAL B 465 " pdb=" N GLY B 466 " pdb=" CA GLY B 466 " ideal model delta sigma weight residual 120.14 123.57 -3.43 1.25e+00 6.40e-01 7.53e+00 angle pdb=" C ASN A 255 " pdb=" N GLU A 256 " pdb=" CA GLU A 256 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.86e+00 ... (remaining 33127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 13776 16.79 - 33.59: 716 33.59 - 50.38: 143 50.38 - 67.17: 24 67.17 - 83.97: 2 Dihedral angle restraints: 14661 sinusoidal: 5622 harmonic: 9039 Sorted by residual: dihedral pdb=" CA TYR B 731 " pdb=" C TYR B 731 " pdb=" N TYR B 732 " pdb=" CA TYR B 732 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LYS B 704 " pdb=" C LYS B 704 " pdb=" N GLU B 705 " pdb=" CA GLU B 705 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA SER A 60 " pdb=" C SER A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 14658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2249 0.028 - 0.057: 1100 0.057 - 0.085: 343 0.085 - 0.114: 206 0.114 - 0.142: 44 Chirality restraints: 3942 Sorted by residual: chirality pdb=" CA ILE B 169 " pdb=" N ILE B 169 " pdb=" C ILE B 169 " pdb=" CB ILE B 169 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA PHE B 460 " pdb=" N PHE B 460 " pdb=" C PHE B 460 " pdb=" CB PHE B 460 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA THR B 64 " pdb=" N THR B 64 " pdb=" C THR B 64 " pdb=" CB THR B 64 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 3939 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 60 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C SER A 60 " -0.037 2.00e-02 2.50e+03 pdb=" O SER A 60 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A 61 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 662 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO B 663 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 663 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 663 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 59 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ALA A 59 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA A 59 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 60 " -0.010 2.00e-02 2.50e+03 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 803 2.71 - 3.26: 25110 3.26 - 3.81: 40472 3.81 - 4.35: 49245 4.35 - 4.90: 87507 Nonbonded interactions: 203137 Sorted by model distance: nonbonded pdb=" NZ LYS C 684 " pdb=" OD2 ASP C 692 " model vdw 2.166 2.520 nonbonded pdb=" OH TYR B 36 " pdb=" OH TYR B 920 " model vdw 2.180 2.440 nonbonded pdb=" O TYR C 858 " pdb=" OG SER C 862 " model vdw 2.185 2.440 nonbonded pdb=" O ILE B 456 " pdb=" OG SER B 459 " model vdw 2.186 2.440 nonbonded pdb=" OG1 THR C 43 " pdb=" OG SER C 132 " model vdw 2.188 2.440 ... (remaining 203132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 502 or (resid 503 and (name N or \ name CA or name C or name O or name CB )) or resid 504 or (resid 505 and (name \ N or name CA or name C or name O or name CB )) or resid 506 through 702 or (resi \ d 703 and (name N or name CA or name C or name O or name CB )) or resid 704 thro \ ugh 1032)) selection = (chain 'B' and (resid 1 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 502 or (resid 503 and (name N or \ name CA or name C or name O or name CB )) or resid 504 or (resid 505 and (name \ N or name CA or name C or name O or name CB )) or resid 506 through 1032)) selection = (chain 'C' and (resid 1 through 702 or (resid 703 and (name N or name CA or name \ C or name O or name CB )) or resid 704 through 1032)) } 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: 3.860 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: 10.670 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 65.170 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.110 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.005 0.054 24390 Z= 0.342 Angle : 0.573 8.873 33132 Z= 0.327 Chirality : 0.041 0.142 3942 Planarity : 0.004 0.052 4200 Dihedral : 10.866 83.966 8817 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.74 % Allowed : 6.51 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.59 (0.15), residues: 3090 helix: 2.03 (0.12), residues: 1720 sheet: 0.11 (0.23), residues: 460 loop : -0.25 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 519 HIS 0.004 0.001 HIS C 582 PHE 0.017 0.002 PHE C 740 TYR 0.013 0.002 TYR A 751 ARG 0.003 0.000 ARG A 994 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 543 time to evaluate : 2.846 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: B 1 MET cc_start: 0.6161 (mtp) cc_final: 0.5432 (ptp) REVERT: B 352 VAL cc_start: 0.8644 (t) cc_final: 0.8321 (m) REVERT: B 408 ASP cc_start: 0.7421 (t0) cc_final: 0.6778 (t0) REVERT: B 534 ARG cc_start: 0.7703 (mmm160) cc_final: 0.7336 (mmm160) REVERT: B 542 PHE cc_start: 0.8420 (t80) cc_final: 0.8212 (t80) REVERT: B 731 TYR cc_start: 0.7912 (t80) cc_final: 0.7488 (t80) REVERT: B 891 MET cc_start: 0.8291 (tpp) cc_final: 0.8074 (tpp) REVERT: B 901 PHE cc_start: 0.7539 (m-80) cc_final: 0.7122 (m-10) REVERT: B 955 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.6938 (t80) REVERT: B 985 PHE cc_start: 0.8535 (m-80) cc_final: 0.8191 (m-80) REVERT: A 40 THR cc_start: 0.9082 (m) cc_final: 0.8814 (p) REVERT: A 598 MET cc_start: 0.8210 (mmm) cc_final: 0.7926 (mtp) REVERT: A 981 LEU cc_start: 0.8992 (tp) cc_final: 0.8683 (tp) REVERT: C 412 ILE cc_start: 0.8810 (mt) cc_final: 0.8512 (mt) REVERT: C 474 LEU cc_start: 0.9191 (mt) cc_final: 0.8700 (mt) outliers start: 72 outliers final: 24 residues processed: 594 average time/residue: 0.3345 time to fit residues: 317.1223 Evaluate side-chains 361 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 336 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 752 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 242 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 0.3980 chunk 280 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 ASN B 582 HIS B 597 GLN B 640 GLN B 648 GLN B 680 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 255 ASN A 325 GLN A 582 HIS A 620 ASN A 679 GLN A 741 ASN A 765 ASN A 776 GLN A 795 ASN C 238 GLN C 245 GLN C 277 ASN C 293 ASN C 312 GLN C 325 GLN C 469 GLN C 511 GLN C 679 GLN C 691 GLN C 694 ASN C 917 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24390 Z= 0.196 Angle : 0.542 11.251 33132 Z= 0.285 Chirality : 0.042 0.242 3942 Planarity : 0.004 0.047 4200 Dihedral : 5.081 58.839 3335 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.39 % Allowed : 11.38 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.73 (0.15), residues: 3090 helix: 2.15 (0.12), residues: 1746 sheet: -0.13 (0.23), residues: 452 loop : -0.08 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 853 HIS 0.002 0.001 HIS C 582 PHE 0.022 0.001 PHE B 333 TYR 0.022 0.001 TYR A 886 ARG 0.003 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 393 time to evaluate : 2.783 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: B 1 MET cc_start: 0.5570 (mtp) cc_final: 0.4801 (ptp) REVERT: B 134 SER cc_start: 0.8505 (m) cc_final: 0.8296 (t) REVERT: B 185 MET cc_start: 0.7873 (tpp) cc_final: 0.7033 (tpp) REVERT: B 408 ASP cc_start: 0.7377 (t0) cc_final: 0.7005 (t0) REVERT: B 534 ARG cc_start: 0.7614 (mmm160) cc_final: 0.7253 (mmm160) REVERT: B 540 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8507 (pp) REVERT: B 901 PHE cc_start: 0.7508 (m-80) cc_final: 0.7241 (m-10) REVERT: B 934 LYS cc_start: 0.9029 (tttm) cc_final: 0.8559 (tttm) REVERT: B 955 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7989 (t80) REVERT: B 985 PHE cc_start: 0.8549 (m-80) cc_final: 0.8212 (m-80) REVERT: B 1011 LEU cc_start: 0.9148 (tp) cc_final: 0.8661 (tp) REVERT: B 1015 PHE cc_start: 0.9053 (m-80) cc_final: 0.8628 (m-80) REVERT: A 40 THR cc_start: 0.9007 (m) cc_final: 0.8722 (p) REVERT: A 532 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8809 (mm) REVERT: A 847 ASP cc_start: 0.7807 (p0) cc_final: 0.7440 (p0) REVERT: C 412 ILE cc_start: 0.8771 (mt) cc_final: 0.8492 (mt) REVERT: C 469 GLN cc_start: 0.8346 (mt0) cc_final: 0.8129 (mm-40) REVERT: C 474 LEU cc_start: 0.9141 (mt) cc_final: 0.8677 (mt) REVERT: C 881 ILE cc_start: 0.9169 (mt) cc_final: 0.8945 (mp) REVERT: C 1010 THR cc_start: 0.8875 (t) cc_final: 0.8603 (p) outliers start: 89 outliers final: 47 residues processed: 452 average time/residue: 0.3062 time to fit residues: 229.9412 Evaluate side-chains 377 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 327 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1006 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 233 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 281 optimal weight: 0.8980 chunk 303 optimal weight: 0.5980 chunk 250 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 225 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN A 737 GLN A 741 ASN C 317 ASN C 765 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24390 Z= 0.193 Angle : 0.520 9.753 33132 Z= 0.269 Chirality : 0.042 0.283 3942 Planarity : 0.004 0.071 4200 Dihedral : 4.888 59.572 3326 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.08 % Allowed : 12.90 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.79 (0.15), residues: 3090 helix: 2.21 (0.12), residues: 1746 sheet: -0.17 (0.23), residues: 453 loop : -0.05 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 853 HIS 0.002 0.000 HIS C 582 PHE 0.019 0.001 PHE B 455 TYR 0.022 0.001 TYR A 886 ARG 0.002 0.000 ARG B 994 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 358 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5374 (mtp) cc_final: 0.4631 (ptp) REVERT: B 185 MET cc_start: 0.7858 (tpp) cc_final: 0.6972 (tpp) REVERT: B 408 ASP cc_start: 0.7386 (t0) cc_final: 0.6692 (t0) REVERT: B 517 PHE cc_start: 0.7952 (t80) cc_final: 0.7700 (t80) REVERT: B 534 ARG cc_start: 0.7556 (mmm160) cc_final: 0.7258 (mmm160) REVERT: B 540 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8428 (pp) REVERT: B 731 TYR cc_start: 0.7883 (t80) cc_final: 0.7560 (t80) REVERT: B 934 LYS cc_start: 0.9011 (tttm) cc_final: 0.8326 (tttm) REVERT: B 955 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7483 (t80) REVERT: B 985 PHE cc_start: 0.8597 (m-80) cc_final: 0.8146 (m-80) REVERT: B 1011 LEU cc_start: 0.9101 (tp) cc_final: 0.8514 (tp) REVERT: B 1015 PHE cc_start: 0.9078 (m-80) cc_final: 0.8649 (m-80) REVERT: A 40 THR cc_start: 0.8952 (m) cc_final: 0.8647 (p) REVERT: A 532 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8813 (mm) REVERT: C 412 ILE cc_start: 0.8735 (mt) cc_final: 0.8454 (mt) REVERT: C 474 LEU cc_start: 0.9109 (mt) cc_final: 0.8757 (mt) REVERT: C 876 ILE cc_start: 0.9244 (mt) cc_final: 0.9030 (mt) REVERT: C 881 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8978 (mp) REVERT: C 1010 THR cc_start: 0.8835 (t) cc_final: 0.8584 (p) outliers start: 81 outliers final: 46 residues processed: 413 average time/residue: 0.3015 time to fit residues: 207.1554 Evaluate side-chains 356 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 306 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 134 optimal weight: 0.3980 chunk 188 optimal weight: 0.9990 chunk 282 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN A 737 GLN A 741 ASN C 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 24390 Z= 0.200 Angle : 0.513 13.797 33132 Z= 0.264 Chirality : 0.041 0.177 3942 Planarity : 0.004 0.047 4200 Dihedral : 4.759 59.933 3322 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.16 % Allowed : 13.44 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.81 (0.15), residues: 3090 helix: 2.25 (0.12), residues: 1740 sheet: -0.15 (0.23), residues: 465 loop : -0.08 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 853 HIS 0.002 0.000 HIS C 582 PHE 0.028 0.001 PHE B 455 TYR 0.022 0.001 TYR C1021 ARG 0.003 0.000 ARG C 653 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 342 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5388 (mtp) cc_final: 0.4603 (ptp) REVERT: B 185 MET cc_start: 0.7833 (tpp) cc_final: 0.6974 (tpp) REVERT: B 408 ASP cc_start: 0.7303 (t0) cc_final: 0.6413 (t0) REVERT: B 534 ARG cc_start: 0.7541 (mmm160) cc_final: 0.7161 (mmm160) REVERT: B 540 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8438 (pp) REVERT: B 731 TYR cc_start: 0.7862 (t80) cc_final: 0.7350 (t80) REVERT: B 807 ASP cc_start: 0.7513 (t70) cc_final: 0.7260 (t70) REVERT: B 934 LYS cc_start: 0.9023 (tttm) cc_final: 0.8664 (tttm) REVERT: B 959 ILE cc_start: 0.8976 (tp) cc_final: 0.8687 (pt) REVERT: B 985 PHE cc_start: 0.8628 (m-80) cc_final: 0.8241 (m-80) REVERT: B 1011 LEU cc_start: 0.9034 (tp) cc_final: 0.8437 (tp) REVERT: B 1015 PHE cc_start: 0.9060 (m-80) cc_final: 0.8729 (m-80) REVERT: A 40 THR cc_start: 0.8963 (m) cc_final: 0.8641 (p) REVERT: A 532 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8803 (mm) REVERT: C 412 ILE cc_start: 0.8690 (mt) cc_final: 0.8438 (mt) REVERT: C 474 LEU cc_start: 0.9128 (mt) cc_final: 0.8700 (mt) REVERT: C 881 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8988 (mp) REVERT: C 1010 THR cc_start: 0.8833 (t) cc_final: 0.8629 (p) REVERT: C 1029 TRP cc_start: 0.7801 (t60) cc_final: 0.7576 (t60) outliers start: 83 outliers final: 55 residues processed: 405 average time/residue: 0.3088 time to fit residues: 210.6822 Evaluate side-chains 372 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 314 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 514 ASN Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 0.0170 chunk 254 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN A 741 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24390 Z= 0.221 Angle : 0.523 14.276 33132 Z= 0.268 Chirality : 0.042 0.277 3942 Planarity : 0.004 0.048 4200 Dihedral : 4.691 58.999 3318 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.50 % Allowed : 13.48 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.88 (0.15), residues: 3090 helix: 2.29 (0.12), residues: 1742 sheet: -0.14 (0.23), residues: 452 loop : -0.03 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1029 HIS 0.002 0.001 HIS C 582 PHE 0.020 0.001 PHE A 538 TYR 0.023 0.001 TYR C1021 ARG 0.003 0.000 ARG B 994 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 339 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5437 (mtp) cc_final: 0.4571 (ptp) REVERT: B 185 MET cc_start: 0.7869 (tpp) cc_final: 0.7037 (tpp) REVERT: B 408 ASP cc_start: 0.7367 (t0) cc_final: 0.6503 (t0) REVERT: B 534 ARG cc_start: 0.7505 (mmm160) cc_final: 0.7138 (mmm160) REVERT: B 540 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8408 (pp) REVERT: B 731 TYR cc_start: 0.7877 (t80) cc_final: 0.7450 (t80) REVERT: B 807 ASP cc_start: 0.7535 (t70) cc_final: 0.7266 (t70) REVERT: B 934 LYS cc_start: 0.9019 (tttm) cc_final: 0.8644 (tttm) REVERT: B 985 PHE cc_start: 0.8657 (m-80) cc_final: 0.8250 (m-80) REVERT: B 1011 LEU cc_start: 0.9027 (tp) cc_final: 0.8454 (tp) REVERT: B 1015 PHE cc_start: 0.9034 (m-80) cc_final: 0.8685 (m-80) REVERT: A 40 THR cc_start: 0.9001 (m) cc_final: 0.8674 (p) REVERT: A 437 MET cc_start: 0.8382 (mmm) cc_final: 0.8038 (mmm) REVERT: A 532 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8898 (mm) REVERT: C 131 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8367 (ptpp) REVERT: C 412 ILE cc_start: 0.8722 (mt) cc_final: 0.8462 (mt) REVERT: C 853 TRP cc_start: 0.7192 (m100) cc_final: 0.6651 (m100) REVERT: C 881 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9030 (mp) REVERT: C 1021 TYR cc_start: 0.8277 (t80) cc_final: 0.7962 (t80) REVERT: C 1029 TRP cc_start: 0.7844 (t60) cc_final: 0.7621 (t60) outliers start: 92 outliers final: 64 residues processed: 407 average time/residue: 0.3159 time to fit residues: 213.1987 Evaluate side-chains 376 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 308 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 708 ASN Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 514 ASN Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.9990 chunk 268 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 298 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 138 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 156 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN A 161 ASN A 737 GLN A 741 ASN A 885 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24390 Z= 0.173 Angle : 0.524 14.633 33132 Z= 0.267 Chirality : 0.042 0.254 3942 Planarity : 0.004 0.052 4200 Dihedral : 4.612 59.046 3316 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.16 % Allowed : 14.31 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.90 (0.15), residues: 3090 helix: 2.29 (0.12), residues: 1741 sheet: -0.11 (0.23), residues: 455 loop : 0.01 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1029 HIS 0.002 0.001 HIS C 582 PHE 0.034 0.001 PHE C 513 TYR 0.019 0.001 TYR C1021 ARG 0.004 0.000 ARG C 653 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 353 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5415 (mtp) cc_final: 0.4595 (ptp) REVERT: B 185 MET cc_start: 0.7821 (tpp) cc_final: 0.6955 (tpp) REVERT: B 408 ASP cc_start: 0.7393 (t0) cc_final: 0.6508 (t0) REVERT: B 534 ARG cc_start: 0.7527 (mmm160) cc_final: 0.7146 (mmm160) REVERT: B 731 TYR cc_start: 0.8001 (t80) cc_final: 0.7710 (t80) REVERT: B 807 ASP cc_start: 0.7481 (t70) cc_final: 0.7245 (t70) REVERT: B 901 PHE cc_start: 0.8006 (m-80) cc_final: 0.7661 (m-10) REVERT: B 934 LYS cc_start: 0.8966 (tttm) cc_final: 0.8591 (tttm) REVERT: B 985 PHE cc_start: 0.8657 (m-80) cc_final: 0.8265 (m-80) REVERT: B 1011 LEU cc_start: 0.8990 (tp) cc_final: 0.8706 (tp) REVERT: A 40 THR cc_start: 0.8969 (m) cc_final: 0.8633 (p) REVERT: A 437 MET cc_start: 0.8519 (mmm) cc_final: 0.7909 (mmm) REVERT: A 532 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8867 (mm) REVERT: C 412 ILE cc_start: 0.8698 (mt) cc_final: 0.8422 (mt) REVERT: C 853 TRP cc_start: 0.6992 (m100) cc_final: 0.6628 (m100) REVERT: C 881 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9003 (mp) REVERT: C 1021 TYR cc_start: 0.8201 (t80) cc_final: 0.7903 (t80) outliers start: 83 outliers final: 53 residues processed: 410 average time/residue: 0.3025 time to fit residues: 208.2310 Evaluate side-chains 375 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 320 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 169 optimal weight: 0.0980 chunk 251 optimal weight: 0.8980 chunk 166 optimal weight: 0.2980 chunk 297 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN A 741 ASN A 885 GLN A1027 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24390 Z= 0.176 Angle : 0.523 14.603 33132 Z= 0.267 Chirality : 0.042 0.220 3942 Planarity : 0.004 0.056 4200 Dihedral : 4.545 57.085 3316 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.70 % Allowed : 15.38 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.93 (0.15), residues: 3090 helix: 2.31 (0.12), residues: 1741 sheet: -0.06 (0.23), residues: 454 loop : -0.00 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1029 HIS 0.002 0.001 HIS C 582 PHE 0.018 0.001 PHE C 513 TYR 0.017 0.001 TYR C1021 ARG 0.005 0.000 ARG C 653 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 343 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5426 (mtp) cc_final: 0.4433 (ptp) REVERT: B 185 MET cc_start: 0.7819 (tpp) cc_final: 0.6960 (tpp) REVERT: B 408 ASP cc_start: 0.7331 (t0) cc_final: 0.6629 (t0) REVERT: B 540 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8377 (pp) REVERT: B 731 TYR cc_start: 0.7953 (t80) cc_final: 0.7637 (t80) REVERT: B 807 ASP cc_start: 0.7496 (t70) cc_final: 0.7264 (t70) REVERT: B 934 LYS cc_start: 0.8962 (tttm) cc_final: 0.8644 (tttm) REVERT: B 985 PHE cc_start: 0.8672 (m-80) cc_final: 0.8269 (m-80) REVERT: A 40 THR cc_start: 0.8936 (m) cc_final: 0.8599 (p) REVERT: A 437 MET cc_start: 0.8526 (mmm) cc_final: 0.7854 (mmm) REVERT: C 88 MET cc_start: 0.8643 (tmm) cc_final: 0.8362 (tmm) REVERT: C 412 ILE cc_start: 0.8660 (mt) cc_final: 0.8379 (mt) REVERT: C 881 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.9003 (mp) REVERT: C 1021 TYR cc_start: 0.8181 (t80) cc_final: 0.7893 (t80) outliers start: 71 outliers final: 55 residues processed: 392 average time/residue: 0.3226 time to fit residues: 211.8258 Evaluate side-chains 366 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 309 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 426 ASN Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.0570 chunk 118 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 GLN B 679 GLN A 737 GLN A 741 ASN ** C 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24390 Z= 0.190 Angle : 0.532 13.960 33132 Z= 0.270 Chirality : 0.042 0.250 3942 Planarity : 0.004 0.048 4200 Dihedral : 4.501 53.297 3316 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.01 % Allowed : 15.34 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.15), residues: 3090 helix: 2.30 (0.12), residues: 1742 sheet: -0.06 (0.23), residues: 455 loop : -0.02 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 853 HIS 0.002 0.001 HIS B 582 PHE 0.016 0.001 PHE A 538 TYR 0.016 0.001 TYR C1021 ARG 0.004 0.000 ARG C 653 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 345 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5368 (mtp) cc_final: 0.4377 (ptp) REVERT: B 99 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7448 (t70) REVERT: B 185 MET cc_start: 0.7819 (tpp) cc_final: 0.6993 (tpp) REVERT: B 408 ASP cc_start: 0.7322 (t0) cc_final: 0.6628 (t0) REVERT: B 731 TYR cc_start: 0.7979 (t80) cc_final: 0.7648 (t80) REVERT: B 807 ASP cc_start: 0.7518 (t70) cc_final: 0.7281 (t70) REVERT: B 934 LYS cc_start: 0.8985 (tttm) cc_final: 0.8687 (tttm) REVERT: B 959 ILE cc_start: 0.9070 (mm) cc_final: 0.8855 (mm) REVERT: B 985 PHE cc_start: 0.8609 (m-80) cc_final: 0.8252 (m-80) REVERT: B 1011 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8596 (tp) REVERT: A 40 THR cc_start: 0.8933 (m) cc_final: 0.8589 (p) REVERT: A 437 MET cc_start: 0.8514 (mmm) cc_final: 0.7833 (mmm) REVERT: A 532 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8916 (mm) REVERT: C 88 MET cc_start: 0.8661 (tmm) cc_final: 0.8376 (tmm) REVERT: C 131 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8327 (ptpp) REVERT: C 412 ILE cc_start: 0.8674 (mt) cc_final: 0.8388 (mt) REVERT: C 877 PHE cc_start: 0.8544 (m-80) cc_final: 0.8259 (m-80) REVERT: C 881 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9006 (mp) REVERT: C 1021 TYR cc_start: 0.8171 (t80) cc_final: 0.7891 (t80) outliers start: 79 outliers final: 57 residues processed: 396 average time/residue: 0.2921 time to fit residues: 193.8537 Evaluate side-chains 386 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 324 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 1011 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 426 ASN Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 4.9990 chunk 285 optimal weight: 0.7980 chunk 260 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 250 optimal weight: 0.9990 chunk 262 optimal weight: 0.8980 chunk 276 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN A 679 GLN A 737 GLN A 741 ASN A1027 ASN ** C 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 24390 Z= 0.237 Angle : 0.559 15.085 33132 Z= 0.283 Chirality : 0.043 0.312 3942 Planarity : 0.004 0.051 4200 Dihedral : 4.498 49.604 3316 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.74 % Allowed : 15.87 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.89 (0.15), residues: 3090 helix: 2.28 (0.12), residues: 1741 sheet: -0.06 (0.23), residues: 454 loop : -0.03 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B1029 HIS 0.002 0.001 HIS B 582 PHE 0.031 0.001 PHE B 455 TYR 0.019 0.001 TYR B 530 ARG 0.005 0.000 ARG C 653 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 328 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5430 (mtp) cc_final: 0.4399 (ptp) REVERT: B 185 MET cc_start: 0.7846 (tpp) cc_final: 0.7037 (tpp) REVERT: B 408 ASP cc_start: 0.7289 (t0) cc_final: 0.6490 (t0) REVERT: B 676 MET cc_start: 0.7966 (ttt) cc_final: 0.7671 (ttt) REVERT: B 731 TYR cc_start: 0.8072 (t80) cc_final: 0.7788 (t80) REVERT: B 807 ASP cc_start: 0.7565 (t70) cc_final: 0.7316 (t70) REVERT: B 893 LEU cc_start: 0.8642 (mm) cc_final: 0.8409 (mt) REVERT: B 934 LYS cc_start: 0.8993 (tttm) cc_final: 0.8633 (tttm) REVERT: B 985 PHE cc_start: 0.8646 (m-80) cc_final: 0.8278 (m-80) REVERT: A 40 THR cc_start: 0.8959 (m) cc_final: 0.8614 (p) REVERT: A 437 MET cc_start: 0.8579 (mmm) cc_final: 0.7891 (mmm) REVERT: A 532 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8960 (mm) REVERT: C 131 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8340 (ptpp) REVERT: C 412 ILE cc_start: 0.8695 (mt) cc_final: 0.8425 (mt) REVERT: C 877 PHE cc_start: 0.8562 (m-80) cc_final: 0.8277 (m-80) REVERT: C 881 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9014 (mp) REVERT: C 1021 TYR cc_start: 0.8279 (t80) cc_final: 0.8010 (t80) outliers start: 72 outliers final: 60 residues processed: 379 average time/residue: 0.3069 time to fit residues: 196.2314 Evaluate side-chains 389 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 326 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 426 ASN Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 307 optimal weight: 0.9990 chunk 283 optimal weight: 0.0060 chunk 245 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 GLN A 679 GLN A 737 GLN A 741 ASN A1027 ASN ** C 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24390 Z= 0.192 Angle : 0.559 13.880 33132 Z= 0.280 Chirality : 0.043 0.313 3942 Planarity : 0.004 0.050 4200 Dihedral : 4.461 50.082 3316 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.47 % Allowed : 16.10 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.86 (0.15), residues: 3090 helix: 2.26 (0.12), residues: 1742 sheet: -0.03 (0.23), residues: 454 loop : -0.06 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1029 HIS 0.002 0.001 HIS B 582 PHE 0.023 0.001 PHE B 455 TYR 0.018 0.001 TYR B 530 ARG 0.004 0.000 ARG C 653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 339 time to evaluate : 2.869 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: B 185 MET cc_start: 0.7838 (tpp) cc_final: 0.6967 (tpp) REVERT: B 408 ASP cc_start: 0.7284 (t0) cc_final: 0.6601 (t0) REVERT: B 676 MET cc_start: 0.7988 (ttt) cc_final: 0.7705 (ttt) REVERT: B 731 TYR cc_start: 0.7999 (t80) cc_final: 0.7758 (t80) REVERT: B 807 ASP cc_start: 0.7495 (t70) cc_final: 0.7266 (t70) REVERT: B 925 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8225 (mt) REVERT: B 934 LYS cc_start: 0.9007 (tttm) cc_final: 0.8694 (tttm) REVERT: B 985 PHE cc_start: 0.8672 (m-80) cc_final: 0.8324 (m-80) REVERT: B 1011 LEU cc_start: 0.8800 (tp) cc_final: 0.8405 (tp) REVERT: A 40 THR cc_start: 0.8933 (m) cc_final: 0.8582 (p) REVERT: A 311 MET cc_start: 0.7794 (mmm) cc_final: 0.7532 (mmm) REVERT: A 532 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8951 (mm) REVERT: A 944 MET cc_start: 0.7953 (mmm) cc_final: 0.7678 (mmt) REVERT: C 131 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8328 (ptpp) REVERT: C 412 ILE cc_start: 0.8699 (mt) cc_final: 0.8415 (mt) REVERT: C 877 PHE cc_start: 0.8552 (m-80) cc_final: 0.8301 (m-80) REVERT: C 881 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8999 (mp) REVERT: C 1021 TYR cc_start: 0.8215 (t80) cc_final: 0.7982 (t80) outliers start: 65 outliers final: 55 residues processed: 385 average time/residue: 0.3024 time to fit residues: 195.7355 Evaluate side-chains 380 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 321 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 426 ASN Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 3.9990 chunk 261 optimal weight: 0.0030 chunk 75 optimal weight: 1.9990 chunk 226 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 31 optimal weight: 0.0020 chunk 45 optimal weight: 1.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN A 741 ASN A1027 ASN ** C 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.072597 restraints weight = 53649.569| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.78 r_work: 0.2924 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24390 Z= 0.177 Angle : 0.560 14.557 33132 Z= 0.280 Chirality : 0.043 0.322 3942 Planarity : 0.004 0.052 4200 Dihedral : 4.400 50.538 3316 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.51 % Allowed : 16.33 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.87 (0.15), residues: 3090 helix: 2.28 (0.12), residues: 1738 sheet: -0.01 (0.23), residues: 464 loop : -0.08 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B1029 HIS 0.002 0.001 HIS B 582 PHE 0.047 0.001 PHE B 455 TYR 0.017 0.001 TYR B 530 ARG 0.003 0.000 ARG C 653 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5513.97 seconds wall clock time: 100 minutes 31.30 seconds (6031.30 seconds total)