Starting phenix.real_space_refine on Mon Aug 25 10:04:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd1_51241/08_2025/9gd1_51241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd1_51241/08_2025/9gd1_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_2025/9gd1_51241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd1_51241/08_2025/9gd1_51241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gd1_51241/08_2025/9gd1_51241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd1_51241/08_2025/9gd1_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-2.0-5787/lib/python3.9/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: 5.58, 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: 1.98 Conformation dependent library (CDL) restraints added in 603.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.79 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: 11.20 Time building geometry restraints manager: 2.48 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=" 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' DA I-117 " pdb=" P DA I-116 " ideal model delta sigma weight residual 1.607 1.585 0.022 1.50e-02 4.44e+03 2.15e+00 bond pdb=" O3' DT J 128 " pdb=" P DA J 129 " ideal model delta sigma weight residual 1.607 1.585 0.022 1.50e-02 4.44e+03 2.13e+00 bond pdb=" O3' DT J 25 " pdb=" P DA J 26 " ideal model delta sigma weight residual 1.607 1.586 0.021 1.50e-02 4.44e+03 2.05e+00 ... (remaining 29106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 41018 2.87 - 5.75: 511 5.75 - 8.62: 4 8.62 - 11.49: 3 11.49 - 14.36: 3 Bond angle restraints: 41539 Sorted by residual: angle pdb=" O3' DT J 74 " pdb=" C3' DT J 74 " pdb=" C2' DT J 74 " ideal model delta sigma weight residual 111.50 101.87 9.63 1.50e+00 4.44e-01 4.12e+01 angle pdb=" O3' DC J 76 " pdb=" C3' DC J 76 " pdb=" C2' DC J 76 " ideal model delta sigma weight residual 111.50 102.76 8.74 1.50e+00 4.44e-01 3.39e+01 angle pdb=" O3' DC J 75 " pdb=" C3' DC J 75 " pdb=" C2' DC J 75 " ideal model delta sigma weight residual 111.50 102.81 8.69 1.50e+00 4.44e-01 3.36e+01 angle pdb=" O3' DC I-130 " pdb=" C3' DC I-130 " pdb=" C2' DC I-130 " ideal model delta sigma weight residual 111.50 104.06 7.44 1.50e+00 4.44e-01 2.46e+01 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 ... (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 - 0.049: 3118 0.049 - 0.099: 1097 0.099 - 0.148: 440 0.148 - 0.197: 29 0.197 - 0.247: 8 Chirality restraints: 4692 Sorted by residual: chirality pdb=" C3' DT J 74 " pdb=" C4' DT J 74 " pdb=" O3' DT J 74 " pdb=" C2' DT J 74 " both_signs ideal model delta sigma weight residual False -2.66 -2.91 0.25 2.00e-01 2.50e+01 1.52e+00 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 2.35 -2.10 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C3' DA J 26 " pdb=" C4' DA J 26 " pdb=" O3' DA J 26 " pdb=" C2' DA J 26 " both_signs ideal model delta sigma weight residual False -2.66 -2.90 0.24 2.00e-01 2.50e+01 1.39e+00 ... (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: 5.450 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.200 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.415 29112 Z= 0.334 Angle : 0.825 14.365 41539 Z= 0.521 Chirality : 0.056 0.247 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 aren 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 covalent geometry : bond 0.00499 (29111) covalent geometry : angle 0.82474 (41539) hydrogen bonds : bond 0.11430 ( 1703) hydrogen bonds : angle 5.38057 ( 4355) Misc. bond : bond 0.41519 ( 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 : 0.796 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: 0.9023 (mm) REVERT: B 85 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8740 (p0) REVERT: B 93 GLN cc_start: 0.9338 (mm-40) cc_final: 0.8692 (mm-40) REVERT: C 95 LYS cc_start: 0.9818 (ttmt) cc_final: 0.9586 (tmtt) REVERT: D 36 ILE cc_start: 0.9576 (pt) cc_final: 0.9340 (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 64 LYS cc_start: 0.9385 (mtmt) cc_final: 0.9111 (mtmt) 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: 0.9016 (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: 0.9343 (tp30) REVERT: K 65 LEU cc_start: 0.9714 (mp) cc_final: 0.8879 (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: 0.9174 (mmp) REVERT: K 97 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8887 (tt0) REVERT: L 46 ILE cc_start: 0.9615 (pt) cc_final: 0.9366 (mp) REVERT: L 53 GLU cc_start: 0.9273 (tp30) cc_final: 0.8931 (tm-30) REVERT: L 63 GLU cc_start: 0.9034 (tp30) cc_final: 0.8818 (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: 0.8710 (mtp) REVERT: W 720 MET cc_start: 0.8556 (mpp) cc_final: 0.8124 (mpp) REVERT: W 723 MET cc_start: 0.9264 (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: 0.1747 time to fit residues: 105.2166 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 : 0.850 ------------------------------------------------------------------------------- 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: 6.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 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: 20.0000 chunk 103 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN W 254 GLN W 339 GLN W 343 ASN W 653 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.031179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.021816 restraints weight = 309002.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.022468 restraints weight = 155371.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.022846 restraints weight = 100442.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.023182 restraints weight = 76675.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.023337 restraints weight = 63659.952| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 29112 Z= 0.290 Angle : 0.720 7.804 41539 Z= 0.423 Chirality : 0.039 0.182 4692 Planarity : 0.005 0.055 3474 Dihedral : 29.406 179.949 7994 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.76 % Allowed : 12.18 % Favored : 85.06 % 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 aren not related in a simple way. whole: 0.94 (0.18), residues: 2054 helix: 1.18 (0.14), residues: 1331 sheet: 0.98 (0.52), residues: 92 loop : -0.50 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 78 TYR 0.021 0.002 TYR B 88 PHE 0.019 0.002 PHE W 389 TRP 0.011 0.001 TRP W 417 HIS 0.010 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00642 (29111) covalent geometry : angle 0.71972 (41539) hydrogen bonds : bond 0.06355 ( 1703) hydrogen bonds : angle 4.17101 ( 4355) Misc. bond : bond 0.00136 ( 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 318 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 0.767 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: A 120 MET cc_start: 0.8429 (mmm) cc_final: 0.8217 (mmm) REVERT: B 53 GLU cc_start: 0.9337 (mp0) cc_final: 0.9124 (pm20) REVERT: B 92 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8651 (ttp-170) REVERT: B 93 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8882 (mm-40) REVERT: C 95 LYS cc_start: 0.9822 (ttmt) cc_final: 0.9599 (tmtt) REVERT: D 68 GLU cc_start: 0.9666 (tm-30) cc_final: 0.9417 (tm-30) REVERT: D 77 LEU cc_start: 0.9867 (mm) cc_final: 0.9660 (tp) REVERT: E 51 ILE cc_start: 0.9683 (mt) cc_final: 0.9347 (mm) REVERT: E 64 LYS cc_start: 0.9357 (mtmt) cc_final: 0.8964 (pttm) REVERT: E 105 GLU cc_start: 0.9555 (tm-30) cc_final: 0.9352 (tm-30) REVERT: F 44 LYS cc_start: 0.9551 (tttt) cc_final: 0.8990 (ttmm) REVERT: F 64 ASN cc_start: 0.9450 (m-40) cc_final: 0.9099 (m-40) REVERT: F 84 MET cc_start: 0.9590 (mmp) cc_final: 0.8936 (tpp) REVERT: G 56 GLU cc_start: 0.9357 (tt0) cc_final: 0.8887 (mt-10) REVERT: H 48 ASP cc_start: 0.9313 (OUTLIER) cc_final: 0.9063 (p0) REVERT: H 65 ASP cc_start: 0.9025 (t70) cc_final: 0.8653 (t70) REVERT: H 110 GLU cc_start: 0.9628 (tp30) cc_final: 0.9344 (tp30) REVERT: K 65 LEU cc_start: 0.9468 (mp) cc_final: 0.9226 (mt) REVERT: K 68 GLN cc_start: 0.8934 (pp30) cc_final: 0.8715 (pp30) REVERT: K 90 MET cc_start: 0.9341 (mmp) cc_final: 0.8966 (mmp) REVERT: K 103 LEU cc_start: 0.9838 (tp) cc_final: 0.9613 (tt) REVERT: L 53 GLU cc_start: 0.9274 (tp30) cc_final: 0.9044 (tt0) REVERT: L 68 ASP cc_start: 0.9111 (m-30) cc_final: 0.8832 (t0) REVERT: L 93 GLN cc_start: 0.9356 (tp40) cc_final: 0.9027 (tp-100) REVERT: N 68 GLU cc_start: 0.9263 (tt0) cc_final: 0.9019 (tm-30) REVERT: N 113 LYS cc_start: 0.9629 (tmtt) cc_final: 0.9333 (tptt) REVERT: O 120 MET cc_start: 0.9107 (tpp) cc_final: 0.8787 (tpt) REVERT: P 25 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8337 (t0) REVERT: P 63 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8995 (tm-30) REVERT: P 84 MET cc_start: 0.9593 (mmm) cc_final: 0.9151 (mmm) REVERT: P 88 TYR cc_start: 0.9229 (m-80) cc_final: 0.8730 (m-80) REVERT: W 403 MET cc_start: 0.8643 (mtm) cc_final: 0.8390 (mtm) REVERT: W 444 PHE cc_start: 0.9736 (OUTLIER) cc_final: 0.9362 (t80) REVERT: W 720 MET cc_start: 0.8633 (mpp) cc_final: 0.8136 (mpp) REVERT: W 837 MET cc_start: 0.9488 (tpp) cc_final: 0.8977 (tpp) REVERT: W 1028 LEU cc_start: 0.9850 (pt) cc_final: 0.9477 (mt) outliers start: 50 outliers final: 26 residues processed: 301 average time/residue: 0.1475 time to fit residues: 72.7734 Evaluate side-chains 257 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 103 LEU 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 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 K residue 125 GLN Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 112 GLN Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain W residue 207 CYS Chi-restraints excluded: chain W residue 327 ILE Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 594 ILE Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Chi-restraints excluded: chain W residue 1031 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 87 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 ASN ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 520 ASN W 530 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.039534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.031906 restraints weight = 365348.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.032637 restraints weight = 143635.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.033128 restraints weight = 79274.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.033550 restraints weight = 54975.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.033709 restraints weight = 43388.486| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 29112 Z= 0.250 Angle : 0.654 9.870 41539 Z= 0.384 Chirality : 0.037 0.190 4692 Planarity : 0.004 0.062 3474 Dihedral : 29.436 155.260 7987 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.36 % Allowed : 12.79 % Favored : 83.85 % 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 aren not related in a simple way. whole: 1.17 (0.18), residues: 2054 helix: 1.38 (0.14), residues: 1339 sheet: 0.86 (0.52), residues: 94 loop : -0.45 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 77 TYR 0.020 0.002 TYR G 39 PHE 0.024 0.002 PHE W 389 TRP 0.010 0.001 TRP W 417 HIS 0.008 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00543 (29111) covalent geometry : angle 0.65436 (41539) hydrogen bonds : bond 0.04817 ( 1703) hydrogen bonds : angle 4.01016 ( 4355) Misc. bond : bond 0.00156 ( 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 310 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9636 (tt0) cc_final: 0.9200 (tm-30) REVERT: A 94 GLU cc_start: 0.9544 (tp30) cc_final: 0.9329 (tp30) REVERT: A 120 MET cc_start: 0.8622 (mmm) cc_final: 0.8355 (mmm) REVERT: B 63 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8939 (mp0) REVERT: B 93 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8880 (mm-40) REVERT: B 100 PHE cc_start: 0.8604 (m-80) cc_final: 0.8366 (m-80) REVERT: C 56 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.8950 (pp20) REVERT: C 64 GLU cc_start: 0.8893 (tp30) cc_final: 0.8685 (tp30) REVERT: C 95 LYS cc_start: 0.9809 (ttmt) cc_final: 0.9599 (tmtt) REVERT: D 68 GLU cc_start: 0.9643 (tm-30) cc_final: 0.9405 (tm-30) REVERT: D 96 ARG cc_start: 0.9573 (tpp80) cc_final: 0.9145 (tpp80) REVERT: D 98 LEU cc_start: 0.9672 (tp) cc_final: 0.9349 (tt) REVERT: E 64 LYS cc_start: 0.9392 (mtmt) cc_final: 0.8969 (pttt) REVERT: E 105 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9221 (tm-30) REVERT: F 44 LYS cc_start: 0.9510 (tttt) cc_final: 0.8953 (ttmm) REVERT: F 84 MET cc_start: 0.9595 (mmp) cc_final: 0.8970 (tpp) REVERT: G 56 GLU cc_start: 0.9363 (tt0) cc_final: 0.8874 (mt-10) REVERT: G 101 THR cc_start: 0.9542 (m) cc_final: 0.9090 (p) REVERT: H 39 TYR cc_start: 0.9372 (m-80) cc_final: 0.9106 (m-80) REVERT: H 48 ASP cc_start: 0.9302 (m-30) cc_final: 0.9046 (p0) REVERT: H 65 ASP cc_start: 0.8900 (t70) cc_final: 0.8620 (t0) REVERT: H 110 GLU cc_start: 0.9609 (tp30) cc_final: 0.9370 (tp30) REVERT: K 65 LEU cc_start: 0.9492 (mp) cc_final: 0.9148 (mp) REVERT: K 68 GLN cc_start: 0.9001 (pp30) cc_final: 0.8767 (pp30) REVERT: K 103 LEU cc_start: 0.9833 (tp) cc_final: 0.9628 (tt) REVERT: K 124 ILE cc_start: 0.9826 (mp) cc_final: 0.9183 (mp) REVERT: L 59 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9016 (tptt) REVERT: L 63 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8772 (mp0) REVERT: L 68 ASP cc_start: 0.9110 (m-30) cc_final: 0.8793 (t0) REVERT: M 89 ASN cc_start: 0.9531 (m-40) cc_final: 0.9240 (m110) REVERT: N 68 GLU cc_start: 0.9259 (tt0) cc_final: 0.9012 (tm-30) REVERT: N 113 LYS cc_start: 0.9654 (tmtt) cc_final: 0.9390 (tptt) REVERT: O 93 GLN cc_start: 0.9470 (tp40) cc_final: 0.9138 (tp40) REVERT: O 94 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8781 (mm-30) REVERT: P 25 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8329 (t0) REVERT: P 63 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8935 (tm-30) REVERT: P 84 MET cc_start: 0.9568 (mmm) cc_final: 0.9304 (mmm) REVERT: P 88 TYR cc_start: 0.9220 (m-80) cc_final: 0.8895 (m-80) REVERT: W 403 MET cc_start: 0.8897 (mtm) cc_final: 0.8620 (mtm) REVERT: W 444 PHE cc_start: 0.9764 (OUTLIER) cc_final: 0.9378 (t80) REVERT: W 457 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8914 (mpp) REVERT: W 538 MET cc_start: 0.8665 (tpp) cc_final: 0.8361 (tpp) REVERT: W 720 MET cc_start: 0.8812 (mpp) cc_final: 0.8107 (mpp) REVERT: W 790 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7355 (p0) REVERT: W 837 MET cc_start: 0.9475 (tpp) cc_final: 0.8974 (tpt) REVERT: W 1028 LEU cc_start: 0.9853 (pt) cc_final: 0.9407 (mt) REVERT: W 1056 MET cc_start: 0.8979 (mmm) cc_final: 0.8721 (mmm) outliers start: 61 outliers final: 29 residues processed: 291 average time/residue: 0.1593 time to fit residues: 76.4526 Evaluate side-chains 248 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 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 K residue 125 GLN Chi-restraints excluded: chain L residue 59 LYS 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 65 LEU Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 84 PHE 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 207 CYS 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 457 MET Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Chi-restraints excluded: chain W residue 790 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 193 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** 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 = 0.2887 r_free = 0.2887 target = 0.030698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.021512 restraints weight = 311347.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.022093 restraints weight = 155587.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.022473 restraints weight = 99192.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.022775 restraints weight = 75670.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.022867 restraints weight = 63635.469| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 29112 Z= 0.243 Angle : 0.642 11.081 41539 Z= 0.374 Chirality : 0.036 0.229 4692 Planarity : 0.004 0.059 3474 Dihedral : 29.378 138.999 7987 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.03 % Allowed : 14.17 % Favored : 82.80 % 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 aren not related in a simple way. whole: 1.18 (0.18), residues: 2054 helix: 1.44 (0.14), residues: 1337 sheet: 0.42 (0.49), residues: 105 loop : -0.53 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.026 0.002 TYR W1053 PHE 0.012 0.001 PHE W 389 TRP 0.011 0.001 TRP W 417 HIS 0.010 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00533 (29111) covalent geometry : angle 0.64165 (41539) hydrogen bonds : bond 0.04903 ( 1703) hydrogen bonds : angle 3.93107 ( 4355) Misc. bond : bond 0.00265 ( 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 295 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.568 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: 0.9656 (tt0) cc_final: 0.9108 (tm-30) REVERT: A 94 GLU cc_start: 0.9521 (tp30) cc_final: 0.9291 (tp30) REVERT: A 120 MET cc_start: 0.8939 (mmm) cc_final: 0.8582 (mmm) REVERT: B 93 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8848 (mm-40) REVERT: B 100 PHE cc_start: 0.8537 (m-80) cc_final: 0.8296 (m-80) REVERT: C 56 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.8925 (pp20) REVERT: C 94 ASN cc_start: 0.9705 (t0) cc_final: 0.9308 (m-40) REVERT: C 95 LYS cc_start: 0.9813 (ttmt) cc_final: 0.9575 (tmtt) REVERT: D 68 GLU cc_start: 0.9660 (tm-30) cc_final: 0.9425 (tm-30) REVERT: D 96 ARG cc_start: 0.9532 (tpp80) cc_final: 0.9274 (tpp80) REVERT: D 98 LEU cc_start: 0.9678 (tp) cc_final: 0.9451 (tt) REVERT: E 64 LYS cc_start: 0.9353 (mtmt) cc_final: 0.8808 (pttt) REVERT: E 105 GLU cc_start: 0.9441 (tm-30) cc_final: 0.9201 (tm-30) REVERT: F 44 LYS cc_start: 0.9491 (tttt) cc_final: 0.8910 (ttmm) REVERT: F 84 MET cc_start: 0.9597 (mmp) cc_final: 0.8971 (tpp) REVERT: G 56 GLU cc_start: 0.9345 (tt0) cc_final: 0.8964 (tt0) REVERT: G 101 THR cc_start: 0.9589 (m) cc_final: 0.9151 (p) REVERT: H 48 ASP cc_start: 0.9287 (OUTLIER) cc_final: 0.9068 (p0) REVERT: H 65 ASP cc_start: 0.8868 (t70) cc_final: 0.8605 (t0) REVERT: H 96 ARG cc_start: 0.9334 (mmm-85) cc_final: 0.8824 (ttm110) REVERT: H 110 GLU cc_start: 0.9588 (tp30) cc_final: 0.9364 (tp30) REVERT: K 65 LEU cc_start: 0.9493 (mp) cc_final: 0.9092 (mp) REVERT: K 68 GLN cc_start: 0.9022 (pp30) cc_final: 0.8758 (pp30) REVERT: K 90 MET cc_start: 0.9348 (mmp) cc_final: 0.9135 (mmp) REVERT: K 103 LEU cc_start: 0.9829 (tp) cc_final: 0.9616 (tt) REVERT: K 120 MET cc_start: 0.8948 (mmm) cc_final: 0.8703 (mmm) REVERT: L 63 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8694 (mp0) REVERT: L 68 ASP cc_start: 0.9107 (m-30) cc_final: 0.8823 (t0) REVERT: M 89 ASN cc_start: 0.9566 (m-40) cc_final: 0.9299 (m110) REVERT: M 92 GLU cc_start: 0.8581 (pm20) cc_final: 0.8187 (pm20) REVERT: O 94 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8983 (mm-30) REVERT: P 25 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8426 (t0) REVERT: P 63 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8917 (tm-30) REVERT: W 403 MET cc_start: 0.8907 (mtm) cc_final: 0.8670 (mtm) REVERT: W 444 PHE cc_start: 0.9727 (OUTLIER) cc_final: 0.9378 (t80) REVERT: W 697 MET cc_start: 0.9072 (mtm) cc_final: 0.8834 (mtm) REVERT: W 837 MET cc_start: 0.9472 (tpp) cc_final: 0.8959 (tpt) REVERT: W 1056 MET cc_start: 0.9122 (mmm) cc_final: 0.8829 (mmm) outliers start: 55 outliers final: 29 residues processed: 278 average time/residue: 0.1622 time to fit residues: 73.7486 Evaluate side-chains 250 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 THR 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 K residue 125 GLN 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 W residue 207 CYS Chi-restraints excluded: chain W residue 318 GLU Chi-restraints excluded: chain W residue 429 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 27 optimal weight: 0.3980 chunk 244 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 172 optimal weight: 0.0770 chunk 4 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS H 46 HIS ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN W 452 ASN W 622 GLN W 812 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.032100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.022678 restraints weight = 300374.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.023375 restraints weight = 147961.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.023783 restraints weight = 94385.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.024120 restraints weight = 71659.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.024291 restraints weight = 59835.315| |-----------------------------------------------------------------------------| r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3569 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= 0.152 Angle : 0.614 12.958 41539 Z= 0.352 Chirality : 0.034 0.240 4692 Planarity : 0.004 0.060 3474 Dihedral : 29.056 132.027 7987 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.21 % Allowed : 16.21 % Favored : 81.59 % 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 aren not related in a simple way. whole: 1.37 (0.18), residues: 2054 helix: 1.56 (0.14), residues: 1344 sheet: 0.44 (0.49), residues: 104 loop : -0.39 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 129 TYR 0.022 0.001 TYR B 88 PHE 0.017 0.001 PHE N 67 TRP 0.006 0.001 TRP W 311 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00319 (29111) covalent geometry : angle 0.61427 (41539) hydrogen bonds : bond 0.03571 ( 1703) hydrogen bonds : angle 3.65281 ( 4355) Misc. bond : bond 0.00034 ( 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 307 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 267 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9459 (mm) cc_final: 0.9241 (mm) REVERT: A 93 GLN cc_start: 0.9608 (tt0) cc_final: 0.9151 (tm-30) REVERT: A 120 MET cc_start: 0.8812 (mmm) cc_final: 0.8494 (mmm) REVERT: B 63 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8909 (mp0) REVERT: B 93 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8776 (mm-40) REVERT: C 90 ASP cc_start: 0.8650 (t70) cc_final: 0.8414 (t70) REVERT: C 94 ASN cc_start: 0.9672 (t0) cc_final: 0.9248 (m110) REVERT: C 95 LYS cc_start: 0.9800 (ttmt) cc_final: 0.9537 (tmmt) REVERT: D 68 GLU cc_start: 0.9664 (tm-30) cc_final: 0.9424 (tm-30) REVERT: E 64 LYS cc_start: 0.9364 (mtmt) cc_final: 0.8790 (pttt) REVERT: E 90 MET cc_start: 0.9418 (mmp) cc_final: 0.9191 (mtm) REVERT: E 97 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8557 (mt-10) REVERT: E 105 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9192 (tm-30) REVERT: F 44 LYS cc_start: 0.9492 (tttt) cc_final: 0.8894 (ttmm) REVERT: F 53 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8737 (tm-30) REVERT: F 84 MET cc_start: 0.9604 (mmp) cc_final: 0.9002 (tpp) REVERT: G 56 GLU cc_start: 0.9369 (tt0) cc_final: 0.8989 (tt0) REVERT: G 90 ASP cc_start: 0.8840 (t0) cc_final: 0.8611 (t0) REVERT: G 91 GLU cc_start: 0.9378 (pm20) cc_final: 0.8961 (pm20) REVERT: G 101 THR cc_start: 0.9537 (m) cc_final: 0.9082 (p) REVERT: G 104 GLN cc_start: 0.9432 (mt0) cc_final: 0.9116 (mp10) REVERT: H 48 ASP cc_start: 0.9285 (m-30) cc_final: 0.9051 (p0) REVERT: H 65 ASP cc_start: 0.8894 (t70) cc_final: 0.8675 (t70) REVERT: H 96 ARG cc_start: 0.9292 (mmm-85) cc_final: 0.8913 (ttm110) REVERT: H 110 GLU cc_start: 0.9595 (tp30) cc_final: 0.9351 (tp30) REVERT: K 65 LEU cc_start: 0.9449 (mp) cc_final: 0.9058 (mp) REVERT: K 68 GLN cc_start: 0.9014 (pp30) cc_final: 0.8793 (pp30) REVERT: K 120 MET cc_start: 0.8925 (mmm) cc_final: 0.8723 (mmm) REVERT: L 63 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8753 (mp0) REVERT: L 68 ASP cc_start: 0.9086 (m-30) cc_final: 0.8794 (t0) REVERT: M 73 ASN cc_start: 0.8961 (t0) cc_final: 0.8614 (t0) REVERT: M 89 ASN cc_start: 0.9559 (m-40) cc_final: 0.9273 (m110) REVERT: O 94 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8949 (mm-30) REVERT: P 25 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8302 (t0) REVERT: P 63 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8915 (tm-30) REVERT: P 84 MET cc_start: 0.9492 (mmm) cc_final: 0.9162 (mmm) REVERT: P 88 TYR cc_start: 0.9154 (m-80) cc_final: 0.8766 (m-80) REVERT: W 403 MET cc_start: 0.8873 (mtm) cc_final: 0.8637 (mtm) REVERT: W 444 PHE cc_start: 0.9710 (OUTLIER) cc_final: 0.9430 (t80) REVERT: W 457 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8694 (mpp) REVERT: W 559 LEU cc_start: 0.9454 (tp) cc_final: 0.9186 (tp) REVERT: W 560 MET cc_start: 0.8946 (mmm) cc_final: 0.8656 (mmm) REVERT: W 1028 LEU cc_start: 0.9753 (pt) cc_final: 0.9305 (mt) REVERT: W 1056 MET cc_start: 0.9150 (mmm) cc_final: 0.8771 (mmm) REVERT: W 1134 LEU cc_start: 0.9447 (pp) cc_final: 0.9223 (mt) outliers start: 40 outliers final: 18 residues processed: 291 average time/residue: 0.1546 time to fit residues: 74.2038 Evaluate side-chains 258 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 107 THR 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 125 GLN 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 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 444 PHE Chi-restraints excluded: chain W residue 457 MET Chi-restraints excluded: chain W residue 700 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 167 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 224 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 213 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 ASN ** 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 = 0.2905 r_free = 0.2905 target = 0.031167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.021910 restraints weight = 309013.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.022557 restraints weight = 153114.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.023004 restraints weight = 98633.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.023268 restraints weight = 74438.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.023455 restraints weight = 62543.463| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29112 Z= 0.217 Angle : 0.621 11.707 41539 Z= 0.360 Chirality : 0.035 0.203 4692 Planarity : 0.004 0.059 3474 Dihedral : 28.908 119.762 7987 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.59 % Allowed : 17.14 % Favored : 80.26 % 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 aren not related in a simple way. whole: 1.34 (0.18), residues: 2054 helix: 1.55 (0.14), residues: 1348 sheet: 0.43 (0.49), residues: 104 loop : -0.45 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 95 TYR 0.021 0.001 TYR D 118 PHE 0.012 0.001 PHE K 84 TRP 0.007 0.001 TRP W 311 HIS 0.014 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00480 (29111) covalent geometry : angle 0.62111 (41539) hydrogen bonds : bond 0.04301 ( 1703) hydrogen bonds : angle 3.71479 ( 4355) Misc. bond : bond 0.00157 ( 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 279 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.877 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 120 MET cc_start: 0.8877 (mmm) cc_final: 0.8637 (mmm) REVERT: A 125 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8919 (mm-40) REVERT: B 63 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8910 (mp0) REVERT: B 93 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8753 (mm-40) REVERT: C 56 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.8934 (pp20) REVERT: C 90 ASP cc_start: 0.8691 (t70) cc_final: 0.8315 (t70) REVERT: C 94 ASN cc_start: 0.9701 (t0) cc_final: 0.9294 (m-40) REVERT: C 95 LYS cc_start: 0.9799 (ttmt) cc_final: 0.9573 (tmtt) REVERT: D 68 GLU cc_start: 0.9658 (tm-30) cc_final: 0.9418 (tm-30) REVERT: D 96 ARG cc_start: 0.9537 (tpp80) cc_final: 0.9287 (tpp80) REVERT: E 64 LYS cc_start: 0.9389 (mtmt) cc_final: 0.8816 (pttt) REVERT: E 105 GLU cc_start: 0.9434 (tm-30) cc_final: 0.9150 (tm-30) REVERT: F 44 LYS cc_start: 0.9493 (tttt) cc_final: 0.8945 (ttmm) REVERT: F 84 MET cc_start: 0.9601 (mmp) cc_final: 0.8982 (tpp) REVERT: F 92 ARG cc_start: 0.9120 (tpt-90) cc_final: 0.8787 (ttt90) REVERT: G 95 LYS cc_start: 0.9515 (tmmt) cc_final: 0.9308 (tmmt) REVERT: G 101 THR cc_start: 0.9620 (m) cc_final: 0.9193 (p) REVERT: H 48 ASP cc_start: 0.9278 (OUTLIER) cc_final: 0.9045 (p0) REVERT: H 65 ASP cc_start: 0.8880 (t70) cc_final: 0.8676 (t70) REVERT: H 73 GLU cc_start: 0.9303 (tp30) cc_final: 0.8749 (tp30) REVERT: H 96 ARG cc_start: 0.9281 (mmm-85) cc_final: 0.8760 (ttm110) REVERT: H 97 LEU cc_start: 0.9636 (tp) cc_final: 0.9229 (tp) REVERT: H 110 GLU cc_start: 0.9580 (tp30) cc_final: 0.9366 (tp30) REVERT: K 65 LEU cc_start: 0.9481 (mp) cc_final: 0.9135 (mp) REVERT: K 68 GLN cc_start: 0.9051 (pp30) cc_final: 0.8822 (pp30) REVERT: K 120 MET cc_start: 0.8946 (mmm) cc_final: 0.8729 (mmm) REVERT: L 63 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8722 (mp0) REVERT: L 68 ASP cc_start: 0.9122 (m-30) cc_final: 0.8842 (t0) REVERT: M 73 ASN cc_start: 0.8999 (t0) cc_final: 0.8666 (t0) REVERT: P 25 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8254 (t0) REVERT: P 63 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8927 (tm-30) REVERT: P 84 MET cc_start: 0.9467 (mmm) cc_final: 0.9172 (mmm) REVERT: P 88 TYR cc_start: 0.9175 (m-80) cc_final: 0.8783 (m-80) REVERT: W 444 PHE cc_start: 0.9678 (OUTLIER) cc_final: 0.9416 (t80) REVERT: W 445 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8798 (pp20) REVERT: W 802 MET cc_start: 0.9345 (ptp) cc_final: 0.9082 (ptp) REVERT: W 1028 LEU cc_start: 0.9749 (pt) cc_final: 0.9281 (mt) REVERT: W 1056 MET cc_start: 0.9194 (mmm) cc_final: 0.8816 (mmm) outliers start: 47 outliers final: 27 residues processed: 265 average time/residue: 0.1709 time to fit residues: 74.6087 Evaluate side-chains 249 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 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 103 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 126 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 M residue 114 VAL Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 84 PHE 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 318 GLU Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 445 GLU 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: 0.9990 chunk 167 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 187 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 HIS ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 719 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.040335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.032833 restraints weight = 357784.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.033590 restraints weight = 139865.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.034028 restraints weight = 76876.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.034408 restraints weight = 54622.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.034687 restraints weight = 43371.151| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29112 Z= 0.170 Angle : 0.624 14.741 41539 Z= 0.353 Chirality : 0.035 0.227 4692 Planarity : 0.004 0.056 3474 Dihedral : 28.870 108.329 7987 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.15 % Allowed : 18.25 % Favored : 79.60 % 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 aren not related in a simple way. whole: 1.34 (0.18), residues: 2054 helix: 1.55 (0.14), residues: 1347 sheet: 0.43 (0.49), residues: 104 loop : -0.46 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.025 0.001 TYR B 88 PHE 0.010 0.001 PHE B 100 TRP 0.007 0.001 TRP W 417 HIS 0.008 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00372 (29111) covalent geometry : angle 0.62390 (41539) hydrogen bonds : bond 0.03541 ( 1703) hydrogen bonds : angle 3.66048 ( 4355) Misc. bond : bond 0.00083 ( 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 269 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.849 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 73 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8769 (pp20) REVERT: A 93 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.9209 (tm-30) REVERT: A 94 GLU cc_start: 0.9427 (tp30) cc_final: 0.9209 (tp30) REVERT: A 120 MET cc_start: 0.8962 (mmm) cc_final: 0.8562 (mmm) REVERT: A 125 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8933 (mm-40) REVERT: B 60 VAL cc_start: 0.9854 (t) cc_final: 0.9551 (p) REVERT: B 63 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8894 (mp0) REVERT: B 93 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8725 (mm-40) REVERT: C 56 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.8896 (pp20) REVERT: C 90 ASP cc_start: 0.8722 (t70) cc_final: 0.8435 (t70) REVERT: C 95 LYS cc_start: 0.9783 (ttmt) cc_final: 0.9552 (tmmt) REVERT: D 68 GLU cc_start: 0.9631 (tm-30) cc_final: 0.9382 (tm-30) REVERT: D 96 ARG cc_start: 0.9534 (tpp80) cc_final: 0.9220 (tpp80) REVERT: E 64 LYS cc_start: 0.9357 (mtmt) cc_final: 0.8773 (pttt) REVERT: E 90 MET cc_start: 0.9382 (mmp) cc_final: 0.9173 (mtm) REVERT: E 105 GLU cc_start: 0.9430 (tm-30) cc_final: 0.9132 (tm-30) REVERT: F 44 LYS cc_start: 0.9529 (tttt) cc_final: 0.8973 (ttmm) REVERT: F 84 MET cc_start: 0.9570 (mmp) cc_final: 0.8952 (tpp) REVERT: F 92 ARG cc_start: 0.9139 (tpt-90) cc_final: 0.8834 (tpt-90) REVERT: G 95 LYS cc_start: 0.9565 (tmmt) cc_final: 0.9338 (tmmt) REVERT: G 101 THR cc_start: 0.9523 (m) cc_final: 0.9063 (p) REVERT: G 104 GLN cc_start: 0.9413 (mt0) cc_final: 0.9116 (mp10) REVERT: H 34 TYR cc_start: 0.9299 (m-80) cc_final: 0.8854 (m-80) REVERT: H 48 ASP cc_start: 0.9284 (m-30) cc_final: 0.8970 (p0) REVERT: H 65 ASP cc_start: 0.8853 (t70) cc_final: 0.8577 (t70) REVERT: H 73 GLU cc_start: 0.9347 (tp30) cc_final: 0.8920 (tp30) REVERT: H 96 ARG cc_start: 0.9285 (mmm-85) cc_final: 0.9069 (ttm110) REVERT: H 110 GLU cc_start: 0.9577 (tp30) cc_final: 0.9363 (tp30) REVERT: K 65 LEU cc_start: 0.9438 (mp) cc_final: 0.9035 (mp) REVERT: K 68 GLN cc_start: 0.9044 (pp30) cc_final: 0.8841 (pp30) REVERT: K 106 ASP cc_start: 0.8676 (m-30) cc_final: 0.8406 (p0) REVERT: L 63 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8770 (mp0) REVERT: L 68 ASP cc_start: 0.9081 (m-30) cc_final: 0.8859 (t0) REVERT: M 73 ASN cc_start: 0.8880 (t0) cc_final: 0.8546 (t0) REVERT: M 89 ASN cc_start: 0.9519 (m-40) cc_final: 0.9265 (m110) REVERT: N 68 GLU cc_start: 0.9225 (tt0) cc_final: 0.8835 (tm-30) REVERT: P 25 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8154 (t0) REVERT: P 63 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8883 (tm-30) REVERT: P 88 TYR cc_start: 0.9141 (m-80) cc_final: 0.8834 (m-80) REVERT: W 403 MET cc_start: 0.8876 (mtm) cc_final: 0.8596 (mtm) REVERT: W 444 PHE cc_start: 0.9711 (OUTLIER) cc_final: 0.9480 (t80) REVERT: W 538 MET cc_start: 0.8583 (tpp) cc_final: 0.8285 (tpp) REVERT: W 1056 MET cc_start: 0.9225 (mmm) cc_final: 0.8771 (mmm) outliers start: 39 outliers final: 26 residues processed: 258 average time/residue: 0.1762 time to fit residues: 74.3358 Evaluate side-chains 243 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 126 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 64 LYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 84 PHE 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 318 GLU Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN O 76 GLN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.030116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.020961 restraints weight = 318625.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.021585 restraints weight = 161145.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.022011 restraints weight = 104962.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.022289 restraints weight = 79486.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.022443 restraints weight = 66817.741| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 29112 Z= 0.307 Angle : 0.701 11.216 41539 Z= 0.399 Chirality : 0.039 0.212 4692 Planarity : 0.005 0.055 3474 Dihedral : 29.071 111.694 7987 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.59 % Allowed : 18.52 % Favored : 78.89 % 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 aren not related in a simple way. whole: 0.96 (0.18), residues: 2054 helix: 1.26 (0.14), residues: 1350 sheet: 0.25 (0.49), residues: 104 loop : -0.63 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 77 TYR 0.021 0.002 TYR D 80 PHE 0.015 0.002 PHE B 100 TRP 0.011 0.002 TRP W 440 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00673 (29111) covalent geometry : angle 0.70088 (41539) hydrogen bonds : bond 0.06565 ( 1703) hydrogen bonds : angle 4.07537 ( 4355) Misc. bond : bond 0.00162 ( 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 263 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.894 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: 0.9565 (OUTLIER) cc_final: 0.9058 (tm-30) REVERT: A 120 MET cc_start: 0.9021 (mmm) cc_final: 0.8674 (mmm) REVERT: B 63 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8903 (mp0) REVERT: B 93 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8716 (mm-40) REVERT: C 56 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.8962 (pp20) REVERT: C 90 ASP cc_start: 0.8821 (t70) cc_final: 0.8513 (t70) REVERT: C 95 LYS cc_start: 0.9796 (ttmt) cc_final: 0.9590 (tmtt) REVERT: D 73 GLU cc_start: 0.9553 (tp30) cc_final: 0.9285 (tp30) REVERT: E 105 GLU cc_start: 0.9395 (tm-30) cc_final: 0.9111 (tm-30) REVERT: F 44 LYS cc_start: 0.9517 (tttt) cc_final: 0.9038 (ttmm) REVERT: F 84 MET cc_start: 0.9581 (mmp) cc_final: 0.8947 (tpp) REVERT: G 95 LYS cc_start: 0.9597 (tmmt) cc_final: 0.9325 (tmmt) REVERT: H 34 TYR cc_start: 0.9343 (m-80) cc_final: 0.8842 (m-80) REVERT: H 39 TYR cc_start: 0.9418 (m-80) cc_final: 0.8636 (m-80) REVERT: H 65 ASP cc_start: 0.8828 (t70) cc_final: 0.8613 (t70) REVERT: H 73 GLU cc_start: 0.9323 (tp30) cc_final: 0.8979 (tp30) REVERT: H 96 ARG cc_start: 0.9339 (mmm-85) cc_final: 0.9041 (ttm110) REVERT: H 110 GLU cc_start: 0.9586 (tp30) cc_final: 0.9213 (tp30) REVERT: K 94 GLU cc_start: 0.9150 (pm20) cc_final: 0.8911 (pm20) REVERT: K 97 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8530 (mt-10) REVERT: L 63 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8781 (mp0) REVERT: L 68 ASP cc_start: 0.9126 (m-30) cc_final: 0.8881 (t0) REVERT: M 73 ASN cc_start: 0.9052 (t0) cc_final: 0.8734 (t0) REVERT: N 56 MET cc_start: 0.9432 (tpp) cc_final: 0.9020 (mmm) REVERT: N 68 GLU cc_start: 0.9227 (tt0) cc_final: 0.8877 (tm-30) REVERT: P 25 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8171 (t0) REVERT: P 63 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8901 (tm-30) REVERT: P 84 MET cc_start: 0.9363 (mmm) cc_final: 0.9044 (mmm) REVERT: P 88 TYR cc_start: 0.9196 (m-80) cc_final: 0.8798 (m-80) REVERT: W 403 MET cc_start: 0.8867 (mtm) cc_final: 0.8619 (mtm) REVERT: W 444 PHE cc_start: 0.9692 (OUTLIER) cc_final: 0.9430 (t80) REVERT: W 1056 MET cc_start: 0.9204 (mmm) cc_final: 0.8729 (mmm) outliers start: 47 outliers final: 33 residues processed: 250 average time/residue: 0.1769 time to fit residues: 72.4243 Evaluate side-chains 241 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 126 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 M residue 111 ILE Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 84 PHE 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 318 GLU Chi-restraints excluded: chain W residue 327 ILE Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 699 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: 0.8980 chunk 177 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 214 optimal weight: 0.9990 chunk 44 optimal weight: 0.0870 chunk 223 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.039999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.032512 restraints weight = 358717.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.033252 restraints weight = 141908.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.033730 restraints weight = 78268.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.034112 restraints weight = 54456.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034368 restraints weight = 43005.087| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29112 Z= 0.162 Angle : 0.658 13.136 41539 Z= 0.367 Chirality : 0.036 0.337 4692 Planarity : 0.004 0.056 3474 Dihedral : 29.007 104.001 7987 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.71 % Allowed : 20.07 % Favored : 78.22 % 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 aren not related in a simple way. whole: 1.16 (0.18), residues: 2054 helix: 1.42 (0.14), residues: 1342 sheet: 0.17 (0.48), residues: 104 loop : -0.47 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 92 TYR 0.019 0.001 TYR B 88 PHE 0.026 0.001 PHE B 100 TRP 0.010 0.001 TRP W 417 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00352 (29111) covalent geometry : angle 0.65833 (41539) hydrogen bonds : bond 0.03647 ( 1703) hydrogen bonds : angle 3.78117 ( 4355) Misc. bond : bond 0.00071 ( 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 256 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.857 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: 0.9495 (OUTLIER) cc_final: 0.9100 (tm-30) REVERT: A 120 MET cc_start: 0.9051 (mmm) cc_final: 0.8696 (mmm) REVERT: B 60 VAL cc_start: 0.9846 (t) cc_final: 0.9548 (p) REVERT: B 63 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8902 (mp0) REVERT: B 93 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8626 (mm-40) REVERT: C 56 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.8922 (pp20) REVERT: C 72 ASP cc_start: 0.9089 (m-30) cc_final: 0.8879 (p0) REVERT: C 90 ASP cc_start: 0.8716 (t70) cc_final: 0.8438 (t70) REVERT: C 95 LYS cc_start: 0.9780 (ttmt) cc_final: 0.9545 (tmmt) REVERT: D 73 GLU cc_start: 0.9554 (tp30) cc_final: 0.9254 (tp30) REVERT: E 64 LYS cc_start: 0.9353 (mtmt) cc_final: 0.8773 (pttt) REVERT: E 105 GLU cc_start: 0.9406 (tm-30) cc_final: 0.9101 (tm-30) REVERT: F 44 LYS cc_start: 0.9529 (tttt) cc_final: 0.8988 (ttmm) REVERT: F 84 MET cc_start: 0.9567 (mmp) cc_final: 0.8928 (tpp) REVERT: F 92 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8283 (tmm-80) REVERT: G 95 LYS cc_start: 0.9613 (tmmt) cc_final: 0.9322 (tmmt) REVERT: H 34 TYR cc_start: 0.9342 (m-80) cc_final: 0.8824 (m-80) REVERT: H 65 ASP cc_start: 0.8758 (t70) cc_final: 0.8540 (t70) REVERT: H 73 GLU cc_start: 0.9213 (tp30) cc_final: 0.8923 (tp30) REVERT: H 96 ARG cc_start: 0.9294 (mmm-85) cc_final: 0.8976 (ttm110) REVERT: H 110 GLU cc_start: 0.9588 (tp30) cc_final: 0.9375 (tp30) REVERT: K 106 ASP cc_start: 0.8699 (m-30) cc_final: 0.8447 (p0) REVERT: L 63 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8738 (mp0) REVERT: L 68 ASP cc_start: 0.9025 (m-30) cc_final: 0.8821 (t0) REVERT: M 73 ASN cc_start: 0.8973 (t0) cc_final: 0.8639 (t0) REVERT: M 89 ASN cc_start: 0.9515 (m-40) cc_final: 0.9257 (m110) REVERT: N 56 MET cc_start: 0.9511 (tpp) cc_final: 0.8990 (mmm) REVERT: N 68 GLU cc_start: 0.9213 (tt0) cc_final: 0.8799 (tm-30) REVERT: P 25 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8170 (t0) REVERT: P 63 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8888 (tm-30) REVERT: P 84 MET cc_start: 0.9321 (mmm) cc_final: 0.9006 (mmm) REVERT: P 88 TYR cc_start: 0.9148 (m-80) cc_final: 0.8776 (m-80) REVERT: W 403 MET cc_start: 0.8929 (mtm) cc_final: 0.8630 (mtm) REVERT: W 444 PHE cc_start: 0.9738 (OUTLIER) cc_final: 0.9505 (t80) REVERT: W 530 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.8897 (m110) REVERT: W 538 MET cc_start: 0.8441 (tpp) cc_final: 0.8230 (tpp) REVERT: W 802 MET cc_start: 0.9477 (ptp) cc_final: 0.9155 (ptp) REVERT: W 1028 LEU cc_start: 0.9716 (pt) cc_final: 0.9144 (mt) REVERT: W 1056 MET cc_start: 0.9140 (mmm) cc_final: 0.8773 (mmm) outliers start: 31 outliers final: 23 residues processed: 245 average time/residue: 0.1822 time to fit residues: 73.2275 Evaluate side-chains 244 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 130 ILE 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 125 GLN Chi-restraints excluded: chain K residue 126 LEU 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 64 LYS 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 318 GLU Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 530 ASN 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: 0.9980 chunk 78 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN K 68 GLN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.030473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.021282 restraints weight = 315236.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.021930 restraints weight = 158848.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.022334 restraints weight = 103115.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.022615 restraints weight = 78712.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.022729 restraints weight = 66105.112| |-----------------------------------------------------------------------------| r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 29112 Z= 0.257 Angle : 0.692 12.998 41539 Z= 0.388 Chirality : 0.038 0.267 4692 Planarity : 0.004 0.057 3474 Dihedral : 28.963 104.822 7987 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.93 % Allowed : 20.07 % Favored : 78.00 % 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 aren not related in a simple way. whole: 1.07 (0.18), residues: 2054 helix: 1.35 (0.14), residues: 1344 sheet: 0.09 (0.49), residues: 104 loop : -0.51 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 29 TYR 0.019 0.002 TYR B 88 PHE 0.016 0.001 PHE N 67 TRP 0.008 0.001 TRP W 311 HIS 0.010 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00565 (29111) covalent geometry : angle 0.69186 (41539) hydrogen bonds : bond 0.05157 ( 1703) hydrogen bonds : angle 3.98172 ( 4355) Misc. bond : bond 0.00119 ( 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 243 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.754 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: 0.9536 (OUTLIER) cc_final: 0.9220 (tm-30) REVERT: A 120 MET cc_start: 0.9049 (mmm) cc_final: 0.8690 (mmm) REVERT: B 63 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8871 (mp0) REVERT: B 93 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8643 (mm-40) REVERT: C 56 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.8901 (pp20) REVERT: C 90 ASP cc_start: 0.8756 (t70) cc_final: 0.8485 (t70) REVERT: C 95 LYS cc_start: 0.9786 (ttmt) cc_final: 0.9562 (tmmt) REVERT: D 73 GLU cc_start: 0.9549 (tp30) cc_final: 0.9262 (tp30) REVERT: E 64 LYS cc_start: 0.9373 (mtmt) cc_final: 0.8834 (pttt) REVERT: E 90 MET cc_start: 0.9291 (mtm) cc_final: 0.9027 (mmp) REVERT: E 105 GLU cc_start: 0.9402 (tm-30) cc_final: 0.9112 (tm-30) REVERT: F 44 LYS cc_start: 0.9510 (tttt) cc_final: 0.8991 (ttmm) REVERT: F 84 MET cc_start: 0.9557 (mmp) cc_final: 0.8934 (tpp) REVERT: F 92 ARG cc_start: 0.8940 (ttp80) cc_final: 0.8435 (tmm-80) REVERT: G 95 LYS cc_start: 0.9610 (tmmt) cc_final: 0.9317 (tmmt) REVERT: H 34 TYR cc_start: 0.9285 (m-80) cc_final: 0.8791 (m-80) REVERT: H 73 GLU cc_start: 0.9188 (tp30) cc_final: 0.8918 (tp30) REVERT: H 96 ARG cc_start: 0.9318 (mmm-85) cc_final: 0.9030 (ttm110) REVERT: H 110 GLU cc_start: 0.9573 (tp30) cc_final: 0.9196 (tp30) REVERT: K 106 ASP cc_start: 0.8759 (m-30) cc_final: 0.8495 (p0) REVERT: L 63 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8759 (mp0) REVERT: L 68 ASP cc_start: 0.9082 (m-30) cc_final: 0.8880 (t0) REVERT: M 73 ASN cc_start: 0.9014 (t0) cc_final: 0.8695 (t0) REVERT: N 56 MET cc_start: 0.9393 (tpp) cc_final: 0.8974 (mmm) REVERT: N 68 GLU cc_start: 0.9204 (tt0) cc_final: 0.8842 (tm-30) REVERT: P 25 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8225 (t0) REVERT: P 63 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8897 (tm-30) REVERT: P 88 TYR cc_start: 0.9176 (m-80) cc_final: 0.8921 (m-80) REVERT: W 403 MET cc_start: 0.8939 (mtm) cc_final: 0.8663 (mtm) REVERT: W 444 PHE cc_start: 0.9676 (OUTLIER) cc_final: 0.9455 (t80) REVERT: W 538 MET cc_start: 0.8389 (tpp) cc_final: 0.8103 (tpp) REVERT: W 802 MET cc_start: 0.9398 (ptp) cc_final: 0.9129 (ptp) REVERT: W 1028 LEU cc_start: 0.9750 (pt) cc_final: 0.9176 (mt) REVERT: W 1056 MET cc_start: 0.9132 (mmm) cc_final: 0.8743 (mmm) outliers start: 35 outliers final: 26 residues processed: 235 average time/residue: 0.1879 time to fit residues: 71.5264 Evaluate side-chains 234 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 130 ILE 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 H residue 103 LEU Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 114 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 318 GLU Chi-restraints excluded: chain W residue 444 PHE 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: 3.9990 chunk 208 optimal weight: 2.9990 chunk 243 optimal weight: 20.0000 chunk 228 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 143 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** 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 = 0.3035 r_free = 0.3035 target = 0.039814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.032337 restraints weight = 360111.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.033083 restraints weight = 144047.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.033553 restraints weight = 79314.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.033924 restraints weight = 55147.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034221 restraints weight = 43585.255| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29112 Z= 0.167 Angle : 0.679 12.375 41539 Z= 0.377 Chirality : 0.037 0.289 4692 Planarity : 0.004 0.057 3474 Dihedral : 28.952 101.271 7987 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.60 % Allowed : 20.18 % Favored : 78.22 % 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 aren not related in a simple way. whole: 1.12 (0.18), residues: 2054 helix: 1.38 (0.14), residues: 1347 sheet: 0.05 (0.49), residues: 104 loop : -0.47 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 69 TYR 0.017 0.001 TYR D 118 PHE 0.020 0.001 PHE W 414 TRP 0.010 0.001 TRP W 311 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00365 (29111) covalent geometry : angle 0.67885 (41539) hydrogen bonds : bond 0.03775 ( 1703) hydrogen bonds : angle 3.84838 ( 4355) Misc. bond : bond 0.00051 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4678.28 seconds wall clock time: 81 minutes 35.30 seconds (4895.30 seconds total)