Starting phenix.real_space_refine on Sat Aug 8 09:06:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd1_51241/08_2026/9gd1_51241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd1_51241/08_2026/9gd1_51241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gd1_51241/08_2026/9gd1_51241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd1_51241/08_2026/9gd1_51241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gd1_51241/08_2026/9gd1_51241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd1_51241/08_2026/9gd1_51241.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians P 520 5.49 5 Mg 1 5.21 5 S 50 5.16 5 Be 1 3.05 5 C 15743 2.51 5 N 5055 2.21 5 O 6182 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27555 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 763 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 786 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 742 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 5275 Classifications: {'DNA': 259} Link IDs: {'rna3p': 258} Chain: "J" Number of atoms: 5344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 5344 Classifications: {'DNA': 259} Link IDs: {'rna3p': 258} Chain: "K" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 592 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 658 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "M" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "N" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "O" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "W" Number of atoms: 6969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 849, 6969 Classifications: {'peptide': 849} Link IDs: {'PTRANS': 26, 'TRANS': 822} Chain breaks: 7 Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.60, per 1000 atoms: 0.20 Number of scatterers: 27555 At special positions: 0 Unit cell: (127.602, 177.642, 181.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 50 16.00 P 520 15.00 Mg 1 11.99 F 3 9.00 O 6182 8.00 N 5055 7.00 C 15743 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 779.2 milliseconds 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3962 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 19 sheets defined 69.3% alpha, 5.5% beta 259 base pairs and 513 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.160A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.849A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.587A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.438A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.529A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.689A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.544A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.600A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.096A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.129A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.513A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.575A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 77 removed outlier: 3.986A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 removed outlier: 3.831A pdb=" N LEU K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS K 110 " --> pdb=" O ASP K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.537A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 21 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 Processing helix chain 'L' and resid 82 through 97 removed outlier: 3.839A pdb=" N ARG L 95 " --> pdb=" O LYS L 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.151A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA M 69 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 removed outlier: 3.548A pdb=" N LEU M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 100 through 121 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 79 removed outlier: 3.535A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.518A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 29 removed outlier: 3.980A pdb=" N ILE P 26 " --> pdb=" O ARG P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.704A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG P 55 " --> pdb=" O TYR P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 94 Processing helix chain 'W' and resid 205 through 211 Processing helix chain 'W' and resid 221 through 225 Processing helix chain 'W' and resid 229 through 234 Processing helix chain 'W' and resid 238 through 258 removed outlier: 4.004A pdb=" N LEU W 242 " --> pdb=" O GLY W 238 " (cutoff:3.500A) Processing helix chain 'W' and resid 263 through 284 removed outlier: 3.691A pdb=" N GLU W 280 " --> pdb=" O ARG W 276 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 331 removed outlier: 4.574A pdb=" N LYS W 329 " --> pdb=" O THR W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 331 through 344 removed outlier: 3.681A pdb=" N ARG W 341 " --> pdb=" O HIS W 337 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU W 342 " --> pdb=" O PHE W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 347 through 351 Processing helix chain 'W' and resid 377 through 393 Processing helix chain 'W' and resid 406 through 421 Processing helix chain 'W' and resid 433 through 435 No H-bonds generated for 'chain 'W' and resid 433 through 435' Processing helix chain 'W' and resid 436 through 448 Processing helix chain 'W' and resid 459 through 470 Processing helix chain 'W' and resid 491 through 503 removed outlier: 6.063A pdb=" N ALA W 500 " --> pdb=" O LEU W 496 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU W 501 " --> pdb=" O LYS W 497 " (cutoff:3.500A) Processing helix chain 'W' and resid 514 through 518 removed outlier: 3.512A pdb=" N ARG W 517 " --> pdb=" O GLU W 514 " (cutoff:3.500A) Processing helix chain 'W' and resid 523 through 531 Processing helix chain 'W' and resid 548 through 560 removed outlier: 3.521A pdb=" N LEU W 552 " --> pdb=" O ASN W 548 " (cutoff:3.500A) Processing helix chain 'W' and resid 561 through 565 Processing helix chain 'W' and resid 576 through 591 removed outlier: 3.666A pdb=" N GLU W 580 " --> pdb=" O ASP W 576 " (cutoff:3.500A) Processing helix chain 'W' and resid 598 through 603 Processing helix chain 'W' and resid 619 through 631 Processing helix chain 'W' and resid 633 through 639 removed outlier: 4.105A pdb=" N ALA W 639 " --> pdb=" O SER W 635 " (cutoff:3.500A) Processing helix chain 'W' and resid 650 through 661 removed outlier: 3.610A pdb=" N ASN W 660 " --> pdb=" O LYS W 656 " (cutoff:3.500A) Processing helix chain 'W' and resid 662 through 665 Processing helix chain 'W' and resid 667 through 674 Processing helix chain 'W' and resid 675 through 677 No H-bonds generated for 'chain 'W' and resid 675 through 677' Processing helix chain 'W' and resid 678 through 681 Processing helix chain 'W' and resid 682 through 693 Processing helix chain 'W' and resid 694 through 711 Processing helix chain 'W' and resid 720 through 735 Processing helix chain 'W' and resid 746 through 759 Processing helix chain 'W' and resid 771 through 775 Processing helix chain 'W' and resid 794 through 804 removed outlier: 3.909A pdb=" N ASP W 798 " --> pdb=" O ASN W 794 " (cutoff:3.500A) Processing helix chain 'W' and resid 825 through 844 removed outlier: 3.707A pdb=" N GLU W 831 " --> pdb=" O GLU W 827 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU W 839 " --> pdb=" O LYS W 835 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU W 840 " --> pdb=" O LYS W 836 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR W 841 " --> pdb=" O MET W 837 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA W 842 " --> pdb=" O ILE W 838 " (cutoff:3.500A) Processing helix chain 'W' and resid 1011 through 1026 Processing helix chain 'W' and resid 1031 through 1038 Processing helix chain 'W' and resid 1045 through 1072 Processing helix chain 'W' and resid 1129 through 1152 removed outlier: 4.053A pdb=" N LEU W1133 " --> pdb=" O ASN W1129 " (cutoff:3.500A) Processing helix chain 'W' and resid 1154 through 1158 Processing helix chain 'W' and resid 1176 through 1191 Processing helix chain 'W' and resid 1194 through 1201 Processing helix chain 'W' and resid 1202 through 1205 Processing helix chain 'W' and resid 1249 through 1266 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.019A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.526A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.926A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.944A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'M' and resid 42 through 43 removed outlier: 6.639A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AB5, first strand: chain 'M' and resid 100 through 102 removed outlier: 7.150A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB7, first strand: chain 'W' and resid 179 through 182 removed outlier: 4.343A pdb=" N LYS W 216 " --> pdb=" O ASP W 180 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL W 182 " --> pdb=" O LEU W 214 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU W 214 " --> pdb=" O VAL W 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 287 through 298 removed outlier: 6.621A pdb=" N LEU W 308 " --> pdb=" O ILE W 291 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER W 293 " --> pdb=" O GLN W 306 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN W 306 " --> pdb=" O SER W 293 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG W 295 " --> pdb=" O GLN W 304 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN W 304 " --> pdb=" O ARG W 295 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER W 297 " --> pdb=" O THR W 302 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR W 302 " --> pdb=" O SER W 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 453 through 455 removed outlier: 6.182A pdb=" N ILE W 454 " --> pdb=" O LEU W 489 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN W 508 " --> pdb=" O ASN W 536 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N MET W 538 " --> pdb=" O GLN W 508 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET W 510 " --> pdb=" O MET W 538 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE W 540 " --> pdb=" O MET W 510 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL W 512 " --> pdb=" O ILE W 540 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY W 397 " --> pdb=" O ARG W 537 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE W 398 " --> pdb=" O LEU W 595 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 609 through 616 removed outlier: 6.500A pdb=" N VAL W 786 " --> pdb=" O TYR W 817 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU W 819 " --> pdb=" O VAL W 786 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE W 788 " --> pdb=" O LEU W 819 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N SER W 821 " --> pdb=" O ILE W 788 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU W 715 " --> pdb=" O VAL W 787 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL W 714 " --> pdb=" O PHE W 767 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU W 769 " --> pdb=" O VAL W 714 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE W 716 " --> pdb=" O LEU W 769 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN W 739 " --> pdb=" O LEU W 768 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N SER W 770 " --> pdb=" O GLN W 739 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU W 741 " --> pdb=" O SER W 770 " (cutoff:3.500A) 1039 hydrogen bonds defined for protein. 3027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 664 hydrogen bonds 1328 hydrogen bond angles 0 basepair planarities 259 basepair parallelities 513 stacking parallelities Total time for adding SS restraints: 13.48 Time building geometry restraints manager: 2.90 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: 7068 1.34 - 1.45: 7527 1.45 - 1.57: 13388 1.57 - 1.69: 1037 1.69 - 1.81: 91 Bond restraints: 29111 Sorted by residual: bond pdb=" N ARG W 341 " pdb=" CA ARG W 341 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 9.18e+00 bond pdb=" O3' DA I-117 " pdb=" P DA I-116 " ideal model delta sigma weight residual 1.607 1.585 0.022 1.20e-02 6.94e+03 3.37e+00 bond pdb=" O3' DT J 128 " pdb=" P DA J 129 " ideal model delta sigma weight residual 1.607 1.585 0.022 1.20e-02 6.94e+03 3.32e+00 bond pdb=" C LEU D 98 " pdb=" N LEU D 99 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.83e-02 1.25e+03 3.20e+00 bond pdb=" O3' DT J 25 " pdb=" P DA J 26 " ideal model delta sigma weight residual 1.607 1.586 0.021 1.20e-02 6.94e+03 3.20e+00 ... (remaining 29106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 41278 2.87 - 5.75: 254 5.75 - 8.62: 4 8.62 - 11.49: 0 11.49 - 14.36: 3 Bond angle restraints: 41539 Sorted by residual: angle pdb=" F2 BEF W1502 " pdb="BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 119.96 105.60 14.36 3.00e+00 1.11e-01 2.29e+01 angle pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 120.12 106.07 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " pdb=" F2 BEF W1502 " ideal model delta sigma weight residual 119.91 106.35 13.56 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C4' DG I 20 " pdb=" O4' DG I 20 " pdb=" C1' DG I 20 " ideal model delta sigma weight residual 110.10 105.79 4.31 1.00e+00 1.00e+00 1.86e+01 angle pdb=" C4' DG J 20 " pdb=" O4' DG J 20 " pdb=" C1' DG J 20 " ideal model delta sigma weight residual 110.10 106.40 3.70 1.00e+00 1.00e+00 1.37e+01 ... (remaining 41534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 13415 35.87 - 71.74: 2757 71.74 - 107.61: 18 107.61 - 143.47: 1 143.47 - 179.34: 2 Dihedral angle restraints: 16193 sinusoidal: 10074 harmonic: 6119 Sorted by residual: dihedral pdb=" O1B ADP W1501 " pdb=" O3A ADP W1501 " pdb=" PB ADP W1501 " pdb=" PA ADP W1501 " ideal model delta sinusoidal sigma weight residual 300.00 120.65 179.34 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP W1501 " pdb=" O5' ADP W1501 " pdb=" PA ADP W1501 " pdb=" O2A ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 101.06 -161.05 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" CA LEU W 258 " pdb=" C LEU W 258 " pdb=" N ASP W 259 " pdb=" CA ASP W 259 " ideal model delta harmonic sigma weight residual -180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 16190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3326 0.047 - 0.093: 997 0.093 - 0.140: 353 0.140 - 0.186: 14 0.186 - 0.233: 2 Chirality restraints: 4692 Sorted by residual: chirality pdb=" P DG I-173 " pdb=" OP1 DG I-173 " pdb=" OP2 DG I-173 " pdb=" O5' DG I-173 " both_signs ideal model delta sigma weight residual True 2.34 -2.10 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR W1151 " pdb=" N TYR W1151 " pdb=" C TYR W1151 " pdb=" CB TYR W1151 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C4' DA I-157 " pdb=" C5' DA I-157 " pdb=" O4' DA I-157 " pdb=" C3' DA I-157 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 4689 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 55 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ARG B 55 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG B 55 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY B 56 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 52 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C GLU B 52 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU B 52 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU B 53 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR W 443 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C THR W 443 " 0.057 2.00e-02 2.50e+03 pdb=" O THR W 443 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE W 444 " -0.019 2.00e-02 2.50e+03 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 339 2.62 - 3.19: 23724 3.19 - 3.76: 48986 3.76 - 4.33: 67275 4.33 - 4.90: 98124 Nonbonded interactions: 238448 Sorted by model distance: nonbonded pdb=" OD1 ASP W 513 " pdb="MG MG W1503 " model vdw 2.052 2.170 nonbonded pdb=" OE2 GLU W 514 " pdb="MG MG W1503 " model vdw 2.100 2.170 nonbonded pdb=" OD2 ASP W 513 " pdb="MG MG W1503 " model vdw 2.117 2.170 nonbonded pdb=" CG ASP W 513 " pdb="MG MG W1503 " model vdw 2.291 2.400 nonbonded pdb=" OE2 GLU O 50 " pdb=" NE ARG P 39 " model vdw 2.311 3.120 ... (remaining 238443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 41 through 133) selection = (chain 'O' and resid 41 through 133) } ncs_group { reference = (chain 'B' and resid 25 through 97) selection = (chain 'F' and resid 25 through 97) selection = (chain 'L' and resid 25 through 97) selection = (chain 'P' and resid 25 through 97) } ncs_group { reference = (chain 'C' and resid 16 through 110) selection = (chain 'G' and resid 16 through 110) selection = (chain 'M' and resid 16 through 110) } ncs_group { reference = (chain 'D' and resid 32 through 120) selection = (chain 'H' and resid 32 through 120) selection = (chain 'N' and resid 32 through 120) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.230 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 0.415 29112 Z= 0.352 Angle : 0.701 14.365 41539 Z= 0.484 Chirality : 0.048 0.233 4692 Planarity : 0.010 0.117 3474 Dihedral : 25.612 179.344 12231 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.39 % Allowed : 6.28 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2054 helix: -0.13 (0.12), residues: 1323 sheet: 0.95 (0.52), residues: 83 loop : -0.72 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG H 76 TYR 0.026 0.005 TYR W1151 PHE 0.017 0.002 PHE W 389 TRP 0.020 0.005 TRP W 447 HIS 0.013 0.003 HIS W 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.25 (29111) covalent geometry : angle 0.70133 / 0.48 (41539) hydrogen bonds : bond 0.11430 / 7.51 ( 1703) hydrogen bonds : angle 5.38057 / 3.87 ( 4355) Misc. bond : bond 0.41519 / 21.85 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 381 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9636 (mm) cc_final: 0.9423 (tt) REVERT: A 130 ILE cc_start: 0.9425 (mm) cc_final: 0.9022 (mm) REVERT: B 85 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8739 (p0) REVERT: B 93 GLN cc_start: 0.9338 (mm-40) cc_final: 0.8691 (mm-40) REVERT: C 95 LYS cc_start: 0.9818 (ttmt) cc_final: 0.9585 (tmtt) REVERT: D 36 ILE cc_start: 0.9576 (pt) cc_final: 0.9341 (pt) REVERT: D 68 GLU cc_start: 0.9686 (tm-30) cc_final: 0.9459 (tm-30) REVERT: E 51 ILE cc_start: 0.9656 (mt) cc_final: 0.9310 (mm) REVERT: E 76 GLN cc_start: 0.9668 (tt0) cc_final: 0.9441 (tm-30) REVERT: E 130 ILE cc_start: 0.9554 (mm) cc_final: 0.9222 (mt) REVERT: F 44 LYS cc_start: 0.9492 (tttt) cc_final: 0.8938 (ttmm) REVERT: F 64 ASN cc_start: 0.9375 (m110) cc_final: 0.9105 (m-40) REVERT: F 84 MET cc_start: 0.9620 (mmp) cc_final: 0.9402 (tpp) REVERT: G 39 TYR cc_start: 0.9344 (m-80) cc_final: 0.9074 (m-80) REVERT: G 56 GLU cc_start: 0.9385 (tt0) cc_final: 0.9015 (tt0) REVERT: G 90 ASP cc_start: 0.8608 (t0) cc_final: 0.8134 (t0) REVERT: G 92 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9111 (mp0) REVERT: G 100 VAL cc_start: 0.9624 (t) cc_final: 0.9311 (p) REVERT: H 48 ASP cc_start: 0.9347 (m-30) cc_final: 0.9112 (p0) REVERT: H 65 ASP cc_start: 0.8984 (t70) cc_final: 0.8579 (t70) REVERT: H 68 GLU cc_start: 0.9432 (tt0) cc_final: 0.9154 (tm-30) REVERT: H 92 GLN cc_start: 0.9723 (tt0) cc_final: 0.9100 (tm-30) REVERT: H 110 GLU cc_start: 0.9653 (tp30) cc_final: 0.9344 (tp30) REVERT: K 65 LEU cc_start: 0.9714 (mp) cc_final: 0.8878 (mt) REVERT: K 74 ILE cc_start: 0.9863 (mm) cc_final: 0.9590 (tt) REVERT: K 90 MET cc_start: 0.9455 (mmp) cc_final: 0.9175 (mmp) REVERT: K 97 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8888 (tt0) REVERT: L 46 ILE cc_start: 0.9615 (pt) cc_final: 0.9369 (mp) REVERT: L 53 GLU cc_start: 0.9273 (tp30) cc_final: 0.8930 (tm-30) REVERT: L 63 GLU cc_start: 0.9034 (tp30) cc_final: 0.8817 (tp30) REVERT: L 93 GLN cc_start: 0.9286 (tp40) cc_final: 0.9076 (tp-100) REVERT: M 56 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8533 (mm-30) REVERT: N 113 LYS cc_start: 0.9624 (tmtt) cc_final: 0.9334 (tptt) REVERT: P 63 GLU cc_start: 0.9314 (tm-30) cc_final: 0.8989 (tm-30) REVERT: W 387 MET cc_start: 0.9279 (mtp) cc_final: 0.9001 (ttm) REVERT: W 457 MET cc_start: 0.9006 (mtp) cc_final: 0.8678 (mtp) REVERT: W 720 MET cc_start: 0.8556 (mpp) cc_final: 0.8123 (mpp) REVERT: W 723 MET cc_start: 0.9263 (tmm) cc_final: 0.8658 (tmm) REVERT: W 1057 MET cc_start: 0.9319 (mmp) cc_final: 0.9089 (mmm) outliers start: 7 outliers final: 2 residues processed: 387 average time/residue: 0.1887 time to fit residues: 115.1335 Evaluate side-chains 234 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain W residue 407 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN W 343 ASN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 520 ASN W 653 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.031575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.022170 restraints weight = 303607.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.022824 restraints weight = 152281.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.023215 restraints weight = 98367.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.023554 restraints weight = 74696.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.023723 restraints weight = 62236.774| |-----------------------------------------------------------------------------| r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 29112 Z= 0.237 Angle : 0.822 9.535 41539 Z= 0.456 Chirality : 0.051 0.227 4692 Planarity : 0.005 0.053 3474 Dihedral : 29.656 170.327 7994 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.09 % Allowed : 12.68 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2054 helix: 1.04 (0.14), residues: 1332 sheet: 0.87 (0.51), residues: 98 loop : -0.48 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 128 TYR 0.019 0.002 TYR B 51 PHE 0.020 0.002 PHE O 67 TRP 0.012 0.002 TRP W 417 HIS 0.010 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.24 (29111) covalent geometry : angle 0.82208 / 0.46 (41539) hydrogen bonds : bond 0.06607 / 4.45 ( 1703) hydrogen bonds : angle 4.26984 / 3.08 ( 4355) Misc. bond : bond 0.01521 / 0.80 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8494 (mmm) cc_final: 0.8060 (mmm) REVERT: B 63 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8959 (mp0) REVERT: B 93 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8841 (mm-40) REVERT: C 95 LYS cc_start: 0.9828 (ttmt) cc_final: 0.9592 (tmtt) REVERT: D 68 GLU cc_start: 0.9671 (tm-30) cc_final: 0.9419 (tm-30) REVERT: D 96 ARG cc_start: 0.9491 (tpp80) cc_final: 0.9118 (tpp80) REVERT: E 51 ILE cc_start: 0.9695 (mt) cc_final: 0.9296 (mm) REVERT: E 105 GLU cc_start: 0.9549 (tm-30) cc_final: 0.9327 (tm-30) REVERT: F 44 LYS cc_start: 0.9561 (tttt) cc_final: 0.9029 (tppt) REVERT: F 64 ASN cc_start: 0.9437 (m-40) cc_final: 0.8875 (m110) REVERT: F 84 MET cc_start: 0.9608 (mmp) cc_final: 0.8985 (tpp) REVERT: G 39 TYR cc_start: 0.9438 (m-80) cc_final: 0.9192 (m-80) REVERT: G 56 GLU cc_start: 0.9360 (tt0) cc_final: 0.8903 (mt-10) REVERT: G 90 ASP cc_start: 0.8807 (t0) cc_final: 0.8454 (t70) REVERT: G 91 GLU cc_start: 0.9393 (pm20) cc_final: 0.9072 (pm20) REVERT: H 48 ASP cc_start: 0.9327 (m-30) cc_final: 0.9081 (p0) REVERT: H 56 MET cc_start: 0.9544 (tpp) cc_final: 0.9201 (mmm) REVERT: H 65 ASP cc_start: 0.9008 (t70) cc_final: 0.8612 (t70) REVERT: H 110 GLU cc_start: 0.9638 (tp30) cc_final: 0.9346 (tp30) REVERT: K 65 LEU cc_start: 0.9476 (mp) cc_final: 0.9212 (mt) REVERT: K 74 ILE cc_start: 0.9785 (mm) cc_final: 0.9573 (tt) REVERT: K 90 MET cc_start: 0.9368 (mmp) cc_final: 0.8994 (mmp) REVERT: K 120 MET cc_start: 0.8760 (mmm) cc_final: 0.8452 (mmm) REVERT: K 124 ILE cc_start: 0.9797 (mp) cc_final: 0.9423 (mp) REVERT: L 53 GLU cc_start: 0.9244 (tp30) cc_final: 0.9042 (tt0) REVERT: L 63 GLU cc_start: 0.8900 (tp30) cc_final: 0.8668 (tp30) REVERT: L 68 ASP cc_start: 0.9051 (m-30) cc_final: 0.8797 (t0) REVERT: M 89 ASN cc_start: 0.9487 (m-40) cc_final: 0.9190 (m110) REVERT: M 92 GLU cc_start: 0.8491 (mp0) cc_final: 0.7544 (mp0) REVERT: N 68 GLU cc_start: 0.9251 (tt0) cc_final: 0.8988 (tm-30) REVERT: N 113 LYS cc_start: 0.9630 (tmtt) cc_final: 0.9349 (tptt) REVERT: P 25 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8057 (t0) REVERT: P 63 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8970 (tm-30) REVERT: W 387 MET cc_start: 0.9297 (mtp) cc_final: 0.9067 (ttm) REVERT: W 403 MET cc_start: 0.8605 (mtm) cc_final: 0.8356 (mtm) REVERT: W 720 MET cc_start: 0.8640 (mpp) cc_final: 0.8204 (mpp) REVERT: W 1028 LEU cc_start: 0.9836 (pt) cc_final: 0.9460 (mt) outliers start: 38 outliers final: 23 residues processed: 288 average time/residue: 0.1637 time to fit residues: 78.3705 Evaluate side-chains 248 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 112 GLN Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain W residue 327 ILE Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 87 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 30.0000 chunk 79 optimal weight: 40.0000 chunk 115 optimal weight: 20.0000 chunk 112 optimal weight: 30.0000 chunk 212 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN W 339 GLN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 530 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.033327 restraints weight = 355195.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.034125 restraints weight = 138324.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034649 restraints weight = 75130.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035038 restraints weight = 51735.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.035159 restraints weight = 41159.033| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 29112 Z= 0.165 Angle : 0.702 9.837 41539 Z= 0.402 Chirality : 0.048 0.252 4692 Planarity : 0.004 0.062 3474 Dihedral : 29.808 177.107 7988 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.87 % Allowed : 12.02 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2054 helix: 1.40 (0.14), residues: 1330 sheet: 1.03 (0.54), residues: 92 loop : -0.37 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 77 TYR 0.014 0.001 TYR W1259 PHE 0.017 0.001 PHE W 389 TRP 0.008 0.001 TRP W 417 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (29111) covalent geometry : angle 0.70213 / 0.40 (41539) hydrogen bonds : bond 0.04746 / 3.20 ( 1703) hydrogen bonds : angle 3.90678 / 2.83 ( 4355) Misc. bond : bond 0.01810 / 0.95 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9642 (OUTLIER) cc_final: 0.9316 (tm-30) REVERT: A 120 MET cc_start: 0.8865 (mmm) cc_final: 0.8479 (mmm) REVERT: B 93 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8838 (mm-40) REVERT: C 95 LYS cc_start: 0.9814 (ttmt) cc_final: 0.9589 (tmtt) REVERT: D 68 GLU cc_start: 0.9645 (tm-30) cc_final: 0.9386 (tm-30) REVERT: E 51 ILE cc_start: 0.9618 (mt) cc_final: 0.9316 (mm) REVERT: E 105 GLU cc_start: 0.9495 (tm-30) cc_final: 0.9243 (tm-30) REVERT: F 44 LYS cc_start: 0.9529 (tttt) cc_final: 0.8933 (ttmm) REVERT: F 63 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8653 (pp20) REVERT: F 64 ASN cc_start: 0.9381 (m-40) cc_final: 0.8684 (m-40) REVERT: F 84 MET cc_start: 0.9593 (mmp) cc_final: 0.8933 (tpp) REVERT: G 56 GLU cc_start: 0.9362 (tt0) cc_final: 0.8900 (mt-10) REVERT: G 101 THR cc_start: 0.9527 (m) cc_final: 0.9050 (p) REVERT: H 48 ASP cc_start: 0.9287 (OUTLIER) cc_final: 0.9010 (p0) REVERT: H 65 ASP cc_start: 0.8889 (t70) cc_final: 0.8588 (t0) REVERT: H 92 GLN cc_start: 0.9608 (tt0) cc_final: 0.9148 (tm-30) REVERT: H 110 GLU cc_start: 0.9616 (tp30) cc_final: 0.9331 (tp30) REVERT: K 65 LEU cc_start: 0.9384 (mp) cc_final: 0.9134 (mt) REVERT: K 74 ILE cc_start: 0.9774 (mm) cc_final: 0.9568 (tt) REVERT: K 81 ASP cc_start: 0.8553 (p0) cc_final: 0.8205 (m-30) REVERT: K 93 GLN cc_start: 0.9502 (tp40) cc_final: 0.9195 (tp40) REVERT: L 53 GLU cc_start: 0.9232 (tp30) cc_final: 0.8735 (tt0) REVERT: L 68 ASP cc_start: 0.9080 (m-30) cc_final: 0.8809 (t0) REVERT: N 68 GLU cc_start: 0.9254 (tt0) cc_final: 0.8977 (tm-30) REVERT: N 113 LYS cc_start: 0.9635 (tmtt) cc_final: 0.9338 (tptt) REVERT: O 65 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9317 (tp) REVERT: O 93 GLN cc_start: 0.9508 (tp40) cc_final: 0.9104 (mm110) REVERT: O 94 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8231 (mm-30) REVERT: P 25 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8330 (t0) REVERT: P 63 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8935 (tm-30) REVERT: P 84 MET cc_start: 0.9569 (mmm) cc_final: 0.9212 (mmm) REVERT: P 88 TYR cc_start: 0.9136 (m-80) cc_final: 0.8802 (m-80) REVERT: W 403 MET cc_start: 0.8654 (mtm) cc_final: 0.8329 (mtm) REVERT: W 444 PHE cc_start: 0.9758 (OUTLIER) cc_final: 0.9382 (t80) REVERT: W 457 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8865 (mpp) REVERT: W 697 MET cc_start: 0.9236 (mtm) cc_final: 0.8651 (ttm) REVERT: W 720 MET cc_start: 0.8740 (mpp) cc_final: 0.8137 (mpp) REVERT: W 1028 LEU cc_start: 0.9844 (pt) cc_final: 0.9432 (mt) outliers start: 52 outliers final: 18 residues processed: 298 average time/residue: 0.1612 time to fit residues: 79.8239 Evaluate side-chains 250 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 457 MET Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 193 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 91 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 9 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.040856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.033237 restraints weight = 354654.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.034014 restraints weight = 138316.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.034513 restraints weight = 75130.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.034925 restraints weight = 52078.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.035067 restraints weight = 41272.131| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29112 Z= 0.156 Angle : 0.690 11.467 41539 Z= 0.390 Chirality : 0.045 0.219 4692 Planarity : 0.004 0.063 3474 Dihedral : 29.692 161.113 7987 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.48 % Allowed : 13.62 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2054 helix: 1.38 (0.14), residues: 1333 sheet: 0.83 (0.51), residues: 100 loop : -0.27 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 42 TYR 0.027 0.002 TYR G 39 PHE 0.023 0.001 PHE W 389 TRP 0.008 0.001 TRP W 417 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (29111) covalent geometry : angle 0.68982 / 0.39 (41539) hydrogen bonds : bond 0.04572 / 3.07 ( 1703) hydrogen bonds : angle 3.84633 / 2.81 ( 4355) Misc. bond : bond 0.00557 / 0.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9618 (tt0) cc_final: 0.9353 (tm-30) REVERT: A 120 MET cc_start: 0.8894 (mmm) cc_final: 0.8451 (mmm) REVERT: B 63 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8974 (mt-10) REVERT: B 84 MET cc_start: 0.8966 (tpt) cc_final: 0.8764 (mmm) REVERT: B 93 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8798 (mm-40) REVERT: C 95 LYS cc_start: 0.9812 (ttmt) cc_final: 0.9591 (tmtt) REVERT: D 68 GLU cc_start: 0.9641 (tm-30) cc_final: 0.9384 (tm-30) REVERT: D 110 GLU cc_start: 0.9735 (OUTLIER) cc_final: 0.9223 (mt-10) REVERT: E 50 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8877 (mm-30) REVERT: E 105 GLU cc_start: 0.9476 (tm-30) cc_final: 0.9223 (tm-30) REVERT: E 124 ILE cc_start: 0.9606 (OUTLIER) cc_final: 0.9359 (pt) REVERT: F 44 LYS cc_start: 0.9527 (tttt) cc_final: 0.8946 (ttmm) REVERT: F 64 ASN cc_start: 0.9440 (m-40) cc_final: 0.9156 (m-40) REVERT: F 84 MET cc_start: 0.9599 (mmp) cc_final: 0.8954 (tpp) REVERT: G 56 GLU cc_start: 0.9369 (tt0) cc_final: 0.8974 (tt0) REVERT: G 101 THR cc_start: 0.9554 (m) cc_final: 0.9105 (p) REVERT: H 39 TYR cc_start: 0.9344 (m-80) cc_final: 0.9097 (m-80) REVERT: H 48 ASP cc_start: 0.9283 (m-30) cc_final: 0.9018 (p0) REVERT: H 65 ASP cc_start: 0.8883 (t70) cc_final: 0.8633 (t70) REVERT: H 110 GLU cc_start: 0.9603 (tp30) cc_final: 0.9331 (tp30) REVERT: K 65 LEU cc_start: 0.9392 (mp) cc_final: 0.9184 (mt) REVERT: K 74 ILE cc_start: 0.9792 (mm) cc_final: 0.9572 (tt) REVERT: K 81 ASP cc_start: 0.8476 (p0) cc_final: 0.8221 (m-30) REVERT: K 93 GLN cc_start: 0.9424 (tp40) cc_final: 0.9137 (tp40) REVERT: K 120 MET cc_start: 0.8849 (mmm) cc_final: 0.8464 (mmm) REVERT: L 63 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8839 (mp0) REVERT: L 68 ASP cc_start: 0.9072 (m-30) cc_final: 0.8841 (t0) REVERT: M 89 ASN cc_start: 0.9496 (m-40) cc_final: 0.9248 (m110) REVERT: M 112 GLN cc_start: 0.8029 (mt0) cc_final: 0.7722 (mp10) REVERT: N 113 LYS cc_start: 0.9629 (tmtt) cc_final: 0.9346 (tptt) REVERT: O 65 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9264 (tp) REVERT: O 94 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9020 (mm-30) REVERT: P 25 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8256 (t0) REVERT: P 63 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8914 (tm-30) REVERT: P 84 MET cc_start: 0.9539 (mmm) cc_final: 0.9124 (mmm) REVERT: P 88 TYR cc_start: 0.9148 (m-80) cc_final: 0.8766 (m-80) REVERT: W 444 PHE cc_start: 0.9761 (OUTLIER) cc_final: 0.9386 (t80) REVERT: W 457 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8874 (mpp) REVERT: W 697 MET cc_start: 0.9254 (mtm) cc_final: 0.8685 (ttm) REVERT: W 1028 LEU cc_start: 0.9840 (pt) cc_final: 0.9407 (mt) REVERT: W 1057 MET cc_start: 0.9322 (ptp) cc_final: 0.9111 (ptp) outliers start: 45 outliers final: 21 residues processed: 281 average time/residue: 0.1613 time to fit residues: 75.7068 Evaluate side-chains 251 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 457 MET Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 27 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 104 optimal weight: 30.0000 chunk 172 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 812 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.031810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.022342 restraints weight = 290276.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.022948 restraints weight = 148226.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.023329 restraints weight = 95595.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.023624 restraints weight = 72803.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.023828 restraints weight = 61273.985| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29112 Z= 0.157 Angle : 0.663 11.580 41539 Z= 0.377 Chirality : 0.043 0.270 4692 Planarity : 0.004 0.061 3474 Dihedral : 29.638 151.451 7987 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.76 % Allowed : 14.11 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2054 helix: 1.44 (0.14), residues: 1336 sheet: 0.91 (0.52), residues: 95 loop : -0.33 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.024 0.001 TYR B 88 PHE 0.016 0.001 PHE W 389 TRP 0.008 0.001 TRP W 417 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (29111) covalent geometry : angle 0.66344 / 0.38 (41539) hydrogen bonds : bond 0.04326 / 2.90 ( 1703) hydrogen bonds : angle 3.79109 / 2.76 ( 4355) Misc. bond : bond 0.00378 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 251 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9627 (tt0) cc_final: 0.9201 (tm-30) REVERT: A 94 GLU cc_start: 0.9534 (tp30) cc_final: 0.9318 (tp30) REVERT: A 120 MET cc_start: 0.8875 (mmm) cc_final: 0.8571 (mmm) REVERT: B 93 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8763 (mm-40) REVERT: C 94 ASN cc_start: 0.9668 (t0) cc_final: 0.9258 (m-40) REVERT: C 95 LYS cc_start: 0.9817 (ttmt) cc_final: 0.9542 (ttpt) REVERT: D 68 GLU cc_start: 0.9666 (tm-30) cc_final: 0.9422 (tm-30) REVERT: E 105 GLU cc_start: 0.9484 (tm-30) cc_final: 0.9218 (tm-30) REVERT: F 44 LYS cc_start: 0.9505 (tttt) cc_final: 0.8910 (ttmm) REVERT: F 53 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8509 (tm-30) REVERT: F 63 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8680 (pp20) REVERT: F 64 ASN cc_start: 0.9526 (m-40) cc_final: 0.8967 (m-40) REVERT: F 84 MET cc_start: 0.9621 (mmp) cc_final: 0.8970 (tpp) REVERT: G 56 GLU cc_start: 0.9381 (tt0) cc_final: 0.8921 (mt-10) REVERT: G 101 THR cc_start: 0.9553 (m) cc_final: 0.9092 (p) REVERT: H 48 ASP cc_start: 0.9271 (OUTLIER) cc_final: 0.9029 (p0) REVERT: H 65 ASP cc_start: 0.8886 (t70) cc_final: 0.8654 (t70) REVERT: H 110 GLU cc_start: 0.9614 (tp30) cc_final: 0.9357 (tp30) REVERT: K 65 LEU cc_start: 0.9389 (mp) cc_final: 0.9172 (mm) REVERT: K 68 GLN cc_start: 0.8918 (pp30) cc_final: 0.8709 (pp30) REVERT: K 74 ILE cc_start: 0.9793 (mm) cc_final: 0.9578 (tt) REVERT: K 81 ASP cc_start: 0.8581 (p0) cc_final: 0.8336 (m-30) REVERT: K 93 GLN cc_start: 0.9379 (tp40) cc_final: 0.9058 (tp40) REVERT: K 120 MET cc_start: 0.8847 (mmm) cc_final: 0.8480 (mmm) REVERT: L 68 ASP cc_start: 0.9122 (m-30) cc_final: 0.8874 (t0) REVERT: M 73 ASN cc_start: 0.9092 (t0) cc_final: 0.8771 (t0) REVERT: M 92 GLU cc_start: 0.8444 (pm20) cc_final: 0.8049 (pm20) REVERT: N 42 LEU cc_start: 0.9857 (tt) cc_final: 0.9652 (pp) REVERT: N 56 MET cc_start: 0.9450 (mmm) cc_final: 0.9205 (tpp) REVERT: N 86 ILE cc_start: 0.9677 (mt) cc_final: 0.9453 (mt) REVERT: N 113 LYS cc_start: 0.9633 (tmtt) cc_final: 0.9338 (tptt) REVERT: O 65 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9251 (tp) REVERT: O 94 GLU cc_start: 0.9369 (mm-30) cc_final: 0.9070 (mm-30) REVERT: P 25 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8404 (t0) REVERT: W 403 MET cc_start: 0.8908 (mtm) cc_final: 0.8584 (mtm) REVERT: W 444 PHE cc_start: 0.9737 (OUTLIER) cc_final: 0.9379 (t80) REVERT: W 697 MET cc_start: 0.9130 (mtm) cc_final: 0.8657 (ttm) REVERT: W 1057 MET cc_start: 0.9298 (ptp) cc_final: 0.8921 (ptp) REVERT: W 1134 LEU cc_start: 0.9497 (pp) cc_final: 0.9261 (mt) outliers start: 50 outliers final: 25 residues processed: 283 average time/residue: 0.1607 time to fit residues: 75.5004 Evaluate side-chains 259 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 314 LEU Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 754 ILE Chi-restraints excluded: chain W residue 769 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 167 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 213 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.031170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.021702 restraints weight = 300983.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.022339 restraints weight = 153231.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.022751 restraints weight = 100384.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.022976 restraints weight = 76723.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.023168 restraints weight = 65761.043| |-----------------------------------------------------------------------------| r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 29112 Z= 0.203 Angle : 0.697 11.752 41539 Z= 0.392 Chirality : 0.043 0.229 4692 Planarity : 0.004 0.058 3474 Dihedral : 29.656 141.415 7987 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.81 % Allowed : 15.82 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.18), residues: 2054 helix: 1.45 (0.14), residues: 1337 sheet: 0.66 (0.52), residues: 97 loop : -0.37 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.043 0.002 TYR B 88 PHE 0.014 0.001 PHE W 389 TRP 0.009 0.001 TRP W 417 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 (29111) covalent geometry : angle 0.69718 / 0.39 (41539) hydrogen bonds : bond 0.05185 / 3.47 ( 1703) hydrogen bonds : angle 3.88948 / 2.83 ( 4355) Misc. bond : bond 0.00496 / 0.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9665 (OUTLIER) cc_final: 0.9173 (tm-30) REVERT: A 94 GLU cc_start: 0.9552 (tp30) cc_final: 0.9311 (tp30) REVERT: A 120 MET cc_start: 0.8906 (mmm) cc_final: 0.8621 (mmm) REVERT: B 93 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8743 (mm-40) REVERT: C 64 GLU cc_start: 0.9297 (tp30) cc_final: 0.8923 (tp30) REVERT: C 95 LYS cc_start: 0.9818 (ttmt) cc_final: 0.9594 (tmtt) REVERT: D 68 GLU cc_start: 0.9687 (tm-30) cc_final: 0.9474 (tm-30) REVERT: E 105 GLU cc_start: 0.9471 (tm-30) cc_final: 0.9154 (tm-30) REVERT: F 44 LYS cc_start: 0.9526 (tttt) cc_final: 0.8937 (ttmm) REVERT: F 64 ASN cc_start: 0.9524 (m-40) cc_final: 0.9312 (m-40) REVERT: F 84 MET cc_start: 0.9649 (mmp) cc_final: 0.8995 (tpp) REVERT: G 56 GLU cc_start: 0.9348 (tt0) cc_final: 0.8863 (mt-10) REVERT: H 34 TYR cc_start: 0.9304 (m-80) cc_final: 0.9083 (m-80) REVERT: H 48 ASP cc_start: 0.9296 (m-30) cc_final: 0.8958 (p0) REVERT: H 65 ASP cc_start: 0.8884 (t70) cc_final: 0.8582 (t70) REVERT: H 73 GLU cc_start: 0.9261 (tp30) cc_final: 0.9014 (tp30) REVERT: H 110 GLU cc_start: 0.9640 (tp30) cc_final: 0.9393 (tp30) REVERT: K 65 LEU cc_start: 0.9383 (mp) cc_final: 0.9125 (mt) REVERT: K 74 ILE cc_start: 0.9804 (mm) cc_final: 0.9590 (tt) REVERT: K 93 GLN cc_start: 0.9344 (tp40) cc_final: 0.8828 (tp40) REVERT: K 97 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8525 (mt-10) REVERT: K 106 ASP cc_start: 0.9012 (m-30) cc_final: 0.8580 (p0) REVERT: K 120 MET cc_start: 0.8929 (mmm) cc_final: 0.8573 (mmm) REVERT: L 63 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8988 (pm20) REVERT: L 68 ASP cc_start: 0.9191 (m-30) cc_final: 0.8915 (t0) REVERT: M 73 ASN cc_start: 0.9070 (t0) cc_final: 0.8752 (t0) REVERT: M 89 ASN cc_start: 0.9572 (m-40) cc_final: 0.9300 (m110) REVERT: O 94 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9112 (mm-30) REVERT: P 25 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8448 (t0) REVERT: P 84 MET cc_start: 0.9469 (mmm) cc_final: 0.9206 (mmm) REVERT: P 88 TYR cc_start: 0.9228 (m-80) cc_final: 0.8938 (m-80) REVERT: W 403 MET cc_start: 0.8797 (mtm) cc_final: 0.8531 (mtm) REVERT: W 444 PHE cc_start: 0.9764 (OUTLIER) cc_final: 0.9410 (t80) REVERT: W 802 MET cc_start: 0.9414 (ptp) cc_final: 0.9115 (ptp) REVERT: W 837 MET cc_start: 0.9505 (tpp) cc_final: 0.8991 (tpt) REVERT: W 1056 MET cc_start: 0.9113 (mmm) cc_final: 0.8887 (mmm) REVERT: W 1057 MET cc_start: 0.9316 (ptp) cc_final: 0.8924 (ptp) REVERT: W 1134 LEU cc_start: 0.9458 (pp) cc_final: 0.9232 (mt) outliers start: 51 outliers final: 32 residues processed: 260 average time/residue: 0.1586 time to fit residues: 68.5424 Evaluate side-chains 248 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 38 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 127 optimal weight: 0.0970 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN N 92 GLN W 452 ASN W 719 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.031713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.022307 restraints weight = 302860.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.022964 restraints weight = 152307.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.023328 restraints weight = 98579.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.023655 restraints weight = 76005.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.023862 restraints weight = 62798.546| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29112 Z= 0.149 Angle : 0.658 11.118 41539 Z= 0.372 Chirality : 0.042 0.242 4692 Planarity : 0.004 0.060 3474 Dihedral : 29.574 137.966 7987 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.09 % Allowed : 17.53 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.18), residues: 2054 helix: 1.51 (0.14), residues: 1337 sheet: 0.28 (0.50), residues: 105 loop : -0.36 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 423 TYR 0.026 0.001 TYR B 88 PHE 0.012 0.001 PHE L 61 TRP 0.008 0.001 TRP W 311 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (29111) covalent geometry : angle 0.65831 / 0.37 (41539) hydrogen bonds : bond 0.03988 / 2.67 ( 1703) hydrogen bonds : angle 3.75699 / 2.74 ( 4355) Misc. bond : bond 0.00246 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9637 (tt0) cc_final: 0.9176 (tm-30) REVERT: A 94 GLU cc_start: 0.9536 (tp30) cc_final: 0.9279 (tp30) REVERT: A 120 MET cc_start: 0.8902 (mmm) cc_final: 0.8673 (mmm) REVERT: B 93 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8709 (mm-40) REVERT: C 64 GLU cc_start: 0.9219 (tp30) cc_final: 0.8814 (tp30) REVERT: C 95 LYS cc_start: 0.9814 (ttmt) cc_final: 0.9575 (tmtt) REVERT: D 68 GLU cc_start: 0.9673 (tm-30) cc_final: 0.9431 (tm-30) REVERT: E 97 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8643 (mt-10) REVERT: E 105 GLU cc_start: 0.9469 (tm-30) cc_final: 0.9111 (tm-30) REVERT: E 106 ASP cc_start: 0.9418 (m-30) cc_final: 0.8950 (m-30) REVERT: F 44 LYS cc_start: 0.9512 (tttt) cc_final: 0.8919 (ttmm) REVERT: F 63 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8729 (pp20) REVERT: F 64 ASN cc_start: 0.9566 (m-40) cc_final: 0.9082 (m-40) REVERT: F 84 MET cc_start: 0.9628 (mmp) cc_final: 0.8977 (tpp) REVERT: G 56 GLU cc_start: 0.9361 (tt0) cc_final: 0.8969 (tt0) REVERT: G 104 GLN cc_start: 0.9420 (mt0) cc_final: 0.9128 (mp10) REVERT: H 34 TYR cc_start: 0.9313 (m-80) cc_final: 0.9050 (m-80) REVERT: H 48 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.9014 (p0) REVERT: H 56 MET cc_start: 0.9642 (mmm) cc_final: 0.9416 (tpp) REVERT: H 73 GLU cc_start: 0.9255 (tp30) cc_final: 0.8987 (tp30) REVERT: H 96 ARG cc_start: 0.9305 (mmm-85) cc_final: 0.8795 (ttm110) REVERT: H 110 GLU cc_start: 0.9629 (tp30) cc_final: 0.9385 (tp30) REVERT: K 74 ILE cc_start: 0.9805 (mm) cc_final: 0.9576 (tt) REVERT: K 106 ASP cc_start: 0.8932 (m-30) cc_final: 0.8519 (p0) REVERT: K 120 MET cc_start: 0.8952 (mmm) cc_final: 0.8747 (mmm) REVERT: L 68 ASP cc_start: 0.9168 (m-30) cc_final: 0.8850 (t0) REVERT: M 73 ASN cc_start: 0.9025 (t0) cc_final: 0.8699 (t0) REVERT: M 89 ASN cc_start: 0.9564 (m-40) cc_final: 0.9291 (m110) REVERT: M 112 GLN cc_start: 0.8576 (mp10) cc_final: 0.8170 (mp10) REVERT: O 68 GLN cc_start: 0.9562 (pp30) cc_final: 0.9333 (pp30) REVERT: O 94 GLU cc_start: 0.9317 (mm-30) cc_final: 0.9089 (mm-30) REVERT: P 25 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8478 (t0) REVERT: P 84 MET cc_start: 0.9454 (mmm) cc_final: 0.8922 (mmm) REVERT: P 88 TYR cc_start: 0.9185 (m-80) cc_final: 0.8617 (m-80) REVERT: W 403 MET cc_start: 0.8922 (mtm) cc_final: 0.8636 (mtm) REVERT: W 444 PHE cc_start: 0.9741 (OUTLIER) cc_final: 0.9401 (t80) REVERT: W 837 MET cc_start: 0.9477 (tpp) cc_final: 0.8944 (tpt) REVERT: W 1056 MET cc_start: 0.9116 (mmm) cc_final: 0.8868 (mmm) REVERT: W 1057 MET cc_start: 0.9311 (ptp) cc_final: 0.8919 (ptt) outliers start: 38 outliers final: 20 residues processed: 268 average time/residue: 0.1578 time to fit residues: 70.9718 Evaluate side-chains 247 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 699 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 8.9990 chunk 195 optimal weight: 0.8980 chunk 81 optimal weight: 30.0000 chunk 171 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 231 optimal weight: 0.0470 chunk 61 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 chunk 89 optimal weight: 30.0000 chunk 142 optimal weight: 4.9990 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.031411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.022079 restraints weight = 306950.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.022729 restraints weight = 154732.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.023169 restraints weight = 100265.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.023423 restraints weight = 75592.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.023518 restraints weight = 63725.667| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29112 Z= 0.172 Angle : 0.687 13.565 41539 Z= 0.384 Chirality : 0.042 0.226 4692 Planarity : 0.004 0.058 3474 Dihedral : 29.497 131.264 7987 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.04 % Allowed : 18.85 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2054 helix: 1.48 (0.14), residues: 1343 sheet: 0.21 (0.49), residues: 105 loop : -0.34 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 423 TYR 0.026 0.001 TYR B 88 PHE 0.016 0.001 PHE K 67 TRP 0.009 0.001 TRP W 417 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (29111) covalent geometry : angle 0.68738 / 0.38 (41539) hydrogen bonds : bond 0.04471 / 2.99 ( 1703) hydrogen bonds : angle 3.81054 / 2.78 ( 4355) Misc. bond : bond 0.00152 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9630 (tt0) cc_final: 0.9222 (tm-30) REVERT: A 120 MET cc_start: 0.8903 (mmm) cc_final: 0.8671 (mmm) REVERT: B 93 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8706 (mm-40) REVERT: C 64 GLU cc_start: 0.9222 (tp30) cc_final: 0.8825 (tp30) REVERT: C 95 LYS cc_start: 0.9801 (ttmt) cc_final: 0.9535 (ttpt) REVERT: D 68 GLU cc_start: 0.9675 (tm-30) cc_final: 0.9430 (tm-30) REVERT: E 97 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8625 (mt-10) REVERT: E 105 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9098 (tm-30) REVERT: E 106 ASP cc_start: 0.9407 (m-30) cc_final: 0.8937 (m-30) REVERT: F 44 LYS cc_start: 0.9521 (tttt) cc_final: 0.8939 (ttmm) REVERT: F 64 ASN cc_start: 0.9546 (m-40) cc_final: 0.9329 (m-40) REVERT: F 84 MET cc_start: 0.9626 (mmp) cc_final: 0.8979 (tpp) REVERT: G 56 GLU cc_start: 0.9345 (tt0) cc_final: 0.8954 (tt0) REVERT: H 34 TYR cc_start: 0.9334 (m-80) cc_final: 0.9022 (m-80) REVERT: H 48 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.9015 (p0) REVERT: H 56 MET cc_start: 0.9590 (mmm) cc_final: 0.9387 (tpp) REVERT: H 73 GLU cc_start: 0.9274 (tp30) cc_final: 0.9028 (tp30) REVERT: H 96 ARG cc_start: 0.9323 (mmm-85) cc_final: 0.8839 (ttm110) REVERT: H 110 GLU cc_start: 0.9623 (tp30) cc_final: 0.9385 (tp30) REVERT: K 74 ILE cc_start: 0.9821 (mm) cc_final: 0.9564 (tt) REVERT: K 90 MET cc_start: 0.9370 (tpp) cc_final: 0.8587 (tmm) REVERT: K 93 GLN cc_start: 0.9384 (tp40) cc_final: 0.9177 (tp40) REVERT: K 94 GLU cc_start: 0.9141 (pm20) cc_final: 0.7763 (pm20) REVERT: L 68 ASP cc_start: 0.9185 (m-30) cc_final: 0.8884 (t0) REVERT: M 73 ASN cc_start: 0.9004 (t0) cc_final: 0.8672 (t0) REVERT: M 112 GLN cc_start: 0.8527 (mp10) cc_final: 0.8150 (mp10) REVERT: P 25 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8583 (t0) REVERT: P 84 MET cc_start: 0.9444 (mmm) cc_final: 0.8887 (mmm) REVERT: P 88 TYR cc_start: 0.9207 (m-80) cc_final: 0.8635 (m-80) REVERT: W 403 MET cc_start: 0.8850 (mtm) cc_final: 0.8600 (mtm) REVERT: W 444 PHE cc_start: 0.9734 (OUTLIER) cc_final: 0.9422 (t80) REVERT: W 802 MET cc_start: 0.9409 (ptp) cc_final: 0.9130 (ptp) REVERT: W 837 MET cc_start: 0.9512 (tpp) cc_final: 0.8971 (tpt) REVERT: W 1056 MET cc_start: 0.9129 (mmm) cc_final: 0.8825 (mmm) REVERT: W 1057 MET cc_start: 0.9300 (ptp) cc_final: 0.8986 (ptt) outliers start: 37 outliers final: 25 residues processed: 254 average time/residue: 0.1573 time to fit residues: 66.7757 Evaluate side-chains 243 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 148 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 214 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 223 optimal weight: 5.9990 chunk 189 optimal weight: 0.0470 overall best weight: 3.9084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.031154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.021959 restraints weight = 309179.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.022535 restraints weight = 155567.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.022912 restraints weight = 99681.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.023233 restraints weight = 75860.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.023401 restraints weight = 63191.654| |-----------------------------------------------------------------------------| r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29112 Z= 0.196 Angle : 0.708 14.875 41539 Z= 0.396 Chirality : 0.042 0.232 4692 Planarity : 0.004 0.059 3474 Dihedral : 29.537 125.789 7987 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.32 % Allowed : 19.07 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.18), residues: 2054 helix: 1.45 (0.14), residues: 1342 sheet: 0.17 (0.49), residues: 105 loop : -0.39 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.023 0.002 TYR B 88 PHE 0.027 0.002 PHE B 100 TRP 0.008 0.001 TRP W 311 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.20 (29111) covalent geometry : angle 0.70763 / 0.40 (41539) hydrogen bonds : bond 0.04748 / 3.20 ( 1703) hydrogen bonds : angle 3.93302 / 2.87 ( 4355) Misc. bond : bond 0.00213 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9584 (OUTLIER) cc_final: 0.9210 (tm-30) REVERT: A 120 MET cc_start: 0.8950 (mmm) cc_final: 0.8703 (mmm) REVERT: B 93 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8713 (mm-40) REVERT: C 64 GLU cc_start: 0.9220 (tp30) cc_final: 0.8790 (tp30) REVERT: C 95 LYS cc_start: 0.9796 (ttmt) cc_final: 0.9547 (ttpt) REVERT: D 68 GLU cc_start: 0.9662 (tm-30) cc_final: 0.9445 (tm-30) REVERT: E 90 MET cc_start: 0.9313 (mtm) cc_final: 0.9078 (mmp) REVERT: E 97 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8646 (mt-10) REVERT: E 105 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9064 (tm-30) REVERT: E 106 ASP cc_start: 0.9392 (m-30) cc_final: 0.8896 (m-30) REVERT: F 44 LYS cc_start: 0.9502 (tttt) cc_final: 0.8960 (ttmm) REVERT: F 63 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8739 (pp20) REVERT: F 64 ASN cc_start: 0.9570 (m-40) cc_final: 0.9109 (m-40) REVERT: F 84 MET cc_start: 0.9606 (mmp) cc_final: 0.8968 (tpp) REVERT: G 56 GLU cc_start: 0.9349 (tt0) cc_final: 0.8948 (tt0) REVERT: H 34 TYR cc_start: 0.9365 (m-80) cc_final: 0.9011 (m-80) REVERT: H 48 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.9015 (p0) REVERT: H 56 MET cc_start: 0.9554 (mmm) cc_final: 0.9218 (tpp) REVERT: H 73 GLU cc_start: 0.9252 (tp30) cc_final: 0.9033 (tp30) REVERT: H 96 ARG cc_start: 0.9335 (mmm-85) cc_final: 0.8859 (ttm110) REVERT: H 110 GLU cc_start: 0.9590 (tp30) cc_final: 0.9370 (tp30) REVERT: K 74 ILE cc_start: 0.9827 (mm) cc_final: 0.9583 (tt) REVERT: K 90 MET cc_start: 0.9329 (tpp) cc_final: 0.8467 (tmm) REVERT: K 93 GLN cc_start: 0.9370 (tp40) cc_final: 0.9131 (tp40) REVERT: K 94 GLU cc_start: 0.9118 (pm20) cc_final: 0.7585 (pm20) REVERT: L 68 ASP cc_start: 0.9153 (m-30) cc_final: 0.8896 (t0) REVERT: M 73 ASN cc_start: 0.9007 (t0) cc_final: 0.8676 (t0) REVERT: M 89 ASN cc_start: 0.9553 (m-40) cc_final: 0.9292 (m110) REVERT: M 112 GLN cc_start: 0.8513 (mp10) cc_final: 0.8084 (mp10) REVERT: N 56 MET cc_start: 0.9489 (tpp) cc_final: 0.8823 (mmm) REVERT: P 25 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8626 (t0) REVERT: P 84 MET cc_start: 0.9405 (mmm) cc_final: 0.8815 (mmm) REVERT: P 88 TYR cc_start: 0.9201 (m-80) cc_final: 0.8602 (m-80) REVERT: W 403 MET cc_start: 0.8913 (mtm) cc_final: 0.8686 (mtm) REVERT: W 444 PHE cc_start: 0.9704 (OUTLIER) cc_final: 0.9401 (t80) REVERT: W 802 MET cc_start: 0.9376 (ptp) cc_final: 0.9079 (ptp) REVERT: W 837 MET cc_start: 0.9476 (tpp) cc_final: 0.8948 (tpt) REVERT: W 1007 MET cc_start: 0.8116 (mmm) cc_final: 0.7833 (tpt) REVERT: W 1056 MET cc_start: 0.9164 (mmm) cc_final: 0.8858 (mmm) REVERT: W 1057 MET cc_start: 0.9373 (ptp) cc_final: 0.8945 (ptt) outliers start: 42 outliers final: 32 residues processed: 242 average time/residue: 0.1580 time to fit residues: 62.9569 Evaluate side-chains 250 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 240 optimal weight: 6.9990 chunk 78 optimal weight: 40.0000 chunk 218 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 30.0000 chunk 193 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.030259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.021107 restraints weight = 315952.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.021727 restraints weight = 158135.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.022100 restraints weight = 102712.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.022417 restraints weight = 78521.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.022571 restraints weight = 66009.732| |-----------------------------------------------------------------------------| r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 29112 Z= 0.273 Angle : 0.777 19.259 41539 Z= 0.427 Chirality : 0.044 0.245 4692 Planarity : 0.005 0.056 3474 Dihedral : 29.730 118.500 7987 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.15 % Allowed : 19.29 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2054 helix: 1.19 (0.14), residues: 1341 sheet: 0.11 (0.49), residues: 105 loop : -0.56 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 77 TYR 0.024 0.002 TYR D 118 PHE 0.022 0.002 PHE B 100 TRP 0.012 0.002 TRP W 440 HIS 0.008 0.002 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.27 (29111) covalent geometry : angle 0.77674 / 0.43 (41539) hydrogen bonds : bond 0.06503 / 4.37 ( 1703) hydrogen bonds : angle 4.21781 / 3.07 ( 4355) Misc. bond : bond 0.00337 / 0.18 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9629 (tt0) cc_final: 0.9254 (tm-30) REVERT: A 120 MET cc_start: 0.9028 (mmm) cc_final: 0.8753 (mmm) REVERT: B 93 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8737 (mm-40) REVERT: C 64 GLU cc_start: 0.9278 (tp30) cc_final: 0.8861 (tp30) REVERT: C 95 LYS cc_start: 0.9798 (ttmt) cc_final: 0.9598 (tmtt) REVERT: D 68 GLU cc_start: 0.9669 (tm-30) cc_final: 0.9462 (tm-30) REVERT: D 73 GLU cc_start: 0.9556 (tp30) cc_final: 0.9283 (tp30) REVERT: E 90 MET cc_start: 0.9344 (mtm) cc_final: 0.9073 (mmp) REVERT: E 97 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8636 (mt-10) REVERT: E 105 GLU cc_start: 0.9421 (tm-30) cc_final: 0.9047 (tm-30) REVERT: E 106 ASP cc_start: 0.9382 (m-30) cc_final: 0.8883 (m-30) REVERT: E 124 ILE cc_start: 0.9634 (pt) cc_final: 0.9288 (pt) REVERT: F 44 LYS cc_start: 0.9522 (tttt) cc_final: 0.8988 (ttmm) REVERT: F 84 MET cc_start: 0.9611 (mmp) cc_final: 0.9165 (mmm) REVERT: H 34 TYR cc_start: 0.9359 (m-80) cc_final: 0.8903 (m-80) REVERT: H 48 ASP cc_start: 0.9230 (OUTLIER) cc_final: 0.9025 (p0) REVERT: H 96 ARG cc_start: 0.9388 (mmm-85) cc_final: 0.8882 (ttm110) REVERT: H 110 GLU cc_start: 0.9592 (tp30) cc_final: 0.9206 (tp30) REVERT: K 74 ILE cc_start: 0.9823 (mm) cc_final: 0.9585 (tt) REVERT: L 68 ASP cc_start: 0.9186 (m-30) cc_final: 0.8916 (t0) REVERT: M 112 GLN cc_start: 0.8516 (mp10) cc_final: 0.8093 (mp10) REVERT: N 56 MET cc_start: 0.9477 (tpp) cc_final: 0.9088 (mmm) REVERT: N 68 GLU cc_start: 0.9223 (tt0) cc_final: 0.8911 (tm-30) REVERT: P 25 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8564 (t0) REVERT: P 84 MET cc_start: 0.9427 (mmm) cc_final: 0.9115 (mmm) REVERT: P 88 TYR cc_start: 0.9225 (m-80) cc_final: 0.8863 (m-80) REVERT: W 444 PHE cc_start: 0.9717 (OUTLIER) cc_final: 0.9386 (t80) REVERT: W 802 MET cc_start: 0.9374 (ptp) cc_final: 0.9088 (ptp) REVERT: W 837 MET cc_start: 0.9482 (tpp) cc_final: 0.8979 (tpp) REVERT: W 1007 MET cc_start: 0.8112 (mmm) cc_final: 0.7813 (tpt) REVERT: W 1056 MET cc_start: 0.9145 (mmm) cc_final: 0.8790 (mmm) REVERT: W 1057 MET cc_start: 0.9361 (ptp) cc_final: 0.8898 (ptp) outliers start: 39 outliers final: 24 residues processed: 239 average time/residue: 0.1638 time to fit residues: 64.4581 Evaluate side-chains 229 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 181 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 143 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN N 92 GLN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 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 = 0.2912 r_free = 0.2912 target = 0.031344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.022010 restraints weight = 304932.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.022648 restraints weight = 152434.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.023081 restraints weight = 99309.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.023416 restraints weight = 74462.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.023592 restraints weight = 62128.806| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29112 Z= 0.149 Angle : 0.721 20.822 41539 Z= 0.397 Chirality : 0.043 0.243 4692 Planarity : 0.004 0.055 3474 Dihedral : 29.628 111.062 7987 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.60 % Allowed : 20.12 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 2054 helix: 1.32 (0.14), residues: 1340 sheet: 0.14 (0.50), residues: 104 loop : -0.51 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 129 TYR 0.025 0.001 TYR B 88 PHE 0.022 0.001 PHE B 100 TRP 0.009 0.001 TRP W 447 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (29111) covalent geometry : angle 0.72095 / 0.40 (41539) hydrogen bonds : bond 0.04102 / 2.76 ( 1703) hydrogen bonds : angle 3.97725 / 2.90 ( 4355) Misc. bond : bond 0.00113 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4378.91 seconds wall clock time: 76 minutes 20.49 seconds (4580.49 seconds total)