Starting phenix.real_space_refine on Fri Aug 7 07:15:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ix4_60964/08_2026/9ix4_60964_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ix4_60964/08_2026/9ix4_60964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ix4_60964/08_2026/9ix4_60964_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ix4_60964/08_2026/9ix4_60964_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ix4_60964/08_2026/9ix4_60964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ix4_60964/08_2026/9ix4_60964.map" } resolution = 2.96 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= 0.017 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: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 60 5.16 5 C 12582 2.51 5 N 3485 2.21 5 O 3821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19997 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9522 Classifications: {'peptide': 1178} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 38, 'TRANS': 1139} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 9489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9489 Classifications: {'peptide': 1170} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 38, 'TRANS': 1130} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "F" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.34, per 1000 atoms: 0.22 Number of scatterers: 19997 At special positions: 0 Unit cell: (97.86, 125.82, 144.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 49 15.00 O 3821 8.00 N 3485 7.00 C 12582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 680.6 milliseconds 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4466 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 19 sheets defined 54.9% alpha, 9.8% beta 0 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.881A pdb=" N PHE A 6 " --> pdb=" O GLN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.512A pdb=" N THR A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.712A pdb=" N LEU A 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 116 through 136 Processing helix chain 'A' and resid 142 through 169 Processing helix chain 'A' and resid 172 through 179 removed outlier: 4.229A pdb=" N ILE A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.518A pdb=" N LYS A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 213 removed outlier: 3.505A pdb=" N SER A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.573A pdb=" N ASP A 217 " --> pdb=" O PRO A 214 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU A 219 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 220 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.609A pdb=" N LYS A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.519A pdb=" N LEU A 252 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 280 removed outlier: 4.071A pdb=" N LYS A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 304 through 313 removed outlier: 4.619A pdb=" N SER A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.727A pdb=" N LYS A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 420 Proline residue: A 392 - end of helix removed outlier: 3.702A pdb=" N GLN A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 removed outlier: 3.987A pdb=" N ASP A 425 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA A 426 " --> pdb=" O LEU A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 426' Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.509A pdb=" N GLN A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.571A pdb=" N ASP A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 515 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 552 through 555 Processing helix chain 'A' and resid 556 through 564 removed outlier: 4.070A pdb=" N ASP A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 573 removed outlier: 3.804A pdb=" N ALA A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 616 removed outlier: 3.585A pdb=" N TRP A 604 " --> pdb=" O ASN A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 627 through 647 removed outlier: 3.839A pdb=" N ASP A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 683 removed outlier: 3.949A pdb=" N ASP A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 691 removed outlier: 4.440A pdb=" N VAL A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 717 removed outlier: 3.891A pdb=" N GLN A 707 " --> pdb=" O GLY A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 790 through 806 Processing helix chain 'A' and resid 810 through 823 Processing helix chain 'A' and resid 833 through 849 removed outlier: 3.707A pdb=" N TYR A 837 " --> pdb=" O ALA A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.640A pdb=" N THR A 883 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 895 Processing helix chain 'A' and resid 901 through 928 Processing helix chain 'A' and resid 932 through 948 removed outlier: 3.780A pdb=" N VAL A 946 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS A 948 " --> pdb=" O PHE A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 958 Processing helix chain 'A' and resid 960 through 965 removed outlier: 4.128A pdb=" N GLN A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 960 through 965' Processing helix chain 'A' and resid 990 through 993 Processing helix chain 'A' and resid 1020 through 1027 Processing helix chain 'A' and resid 1041 through 1066 removed outlier: 3.562A pdb=" N ASN A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1078 removed outlier: 3.583A pdb=" N TYR A1078 " --> pdb=" O PRO A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1123 removed outlier: 3.919A pdb=" N GLU A1107 " --> pdb=" O ASP A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1177 Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.991A pdb=" N PHE B 6 " --> pdb=" O GLN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 48 removed outlier: 3.585A pdb=" N ILE B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 64 through 76 Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 116 through 136 Processing helix chain 'B' and resid 139 through 169 removed outlier: 3.683A pdb=" N LYS B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 187 through 200 Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 214 through 218 removed outlier: 3.683A pdb=" N ASP B 217 " --> pdb=" O PRO B 214 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 214 through 218' Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 264 through 280 removed outlier: 4.037A pdb=" N GLN B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 300 Processing helix chain 'B' and resid 304 through 312 removed outlier: 4.369A pdb=" N SER B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 331 removed outlier: 3.680A pdb=" N LYS B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 420 Proline residue: B 392 - end of helix removed outlier: 3.553A pdb=" N SER B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.655A pdb=" N GLN B 477 " --> pdb=" O ARG B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.696A pdb=" N ASP B 492 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 515 Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 552 through 555 removed outlier: 3.592A pdb=" N LEU B 555 " --> pdb=" O VAL B 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 555' Processing helix chain 'B' and resid 556 through 564 removed outlier: 3.668A pdb=" N ILE B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 564 " --> pdb=" O ILE B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 removed outlier: 3.690A pdb=" N ALA B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 Processing helix chain 'B' and resid 601 through 616 Processing helix chain 'B' and resid 629 through 646 Processing helix chain 'B' and resid 664 through 667 removed outlier: 3.554A pdb=" N MET B 667 " --> pdb=" O ASP B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 664 through 667' Processing helix chain 'B' and resid 668 through 683 Processing helix chain 'B' and resid 703 through 717 removed outlier: 4.019A pdb=" N VAL B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 732 Processing helix chain 'B' and resid 742 through 749 Processing helix chain 'B' and resid 761 through 764 Processing helix chain 'B' and resid 790 through 806 Processing helix chain 'B' and resid 810 through 823 Processing helix chain 'B' and resid 833 through 849 removed outlier: 3.882A pdb=" N TYR B 837 " --> pdb=" O ALA B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 852 No H-bonds generated for 'chain 'B' and resid 850 through 852' Processing helix chain 'B' and resid 867 through 873 Processing helix chain 'B' and resid 879 through 883 Processing helix chain 'B' and resid 884 through 895 Processing helix chain 'B' and resid 896 through 898 No H-bonds generated for 'chain 'B' and resid 896 through 898' Processing helix chain 'B' and resid 901 through 929 removed outlier: 3.638A pdb=" N ALA B 926 " --> pdb=" O ARG B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 948 removed outlier: 3.732A pdb=" N GLN B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 948 " --> pdb=" O PHE B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 958 Processing helix chain 'B' and resid 1019 through 1027 Processing helix chain 'B' and resid 1041 through 1066 removed outlier: 3.682A pdb=" N ASN B1047 " --> pdb=" O ALA B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1078 removed outlier: 3.536A pdb=" N ASN B1077 " --> pdb=" O LYS B1074 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR B1078 " --> pdb=" O PRO B1075 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1074 through 1078' Processing helix chain 'B' and resid 1103 through 1123 Processing helix chain 'B' and resid 1165 through 1176 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.692A pdb=" N ALA A 88 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THR A 227 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A 53 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU A 226 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE A 55 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 54 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET A 23 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER A 523 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU A 25 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 22 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA5, first strand: chain 'A' and resid 576 through 581 removed outlier: 6.184A pdb=" N LYS A 577 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N MET A 865 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU A 579 " --> pdb=" O MET A 865 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 692 through 695 removed outlier: 3.529A pdb=" N LEU A 725 " --> pdb=" O ARG A 694 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 726 " --> pdb=" O GLY A 655 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 750 through 751 Processing sheet with id=AA8, first strand: chain 'A' and resid 994 through 996 removed outlier: 6.855A pdb=" N GLN A 994 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 983 " --> pdb=" O VAL A1004 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1083 through 1085 removed outlier: 6.233A pdb=" N VAL A1090 " --> pdb=" O ILE A1129 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE A1131 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP A1092 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE A1133 " --> pdb=" O ASP A1092 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N LYS A1094 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N ARG A1127 " --> pdb=" O ILE A1149 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N GLU A1151 " --> pdb=" O ARG A1127 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ILE A1129 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N SER A1153 " --> pdb=" O ILE A1129 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N ILE A1131 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU A1155 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE A1133 " --> pdb=" O LEU A1155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.609A pdb=" N ALA B 88 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N THR B 227 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE B 54 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET B 23 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER B 523 " --> pdb=" O MET B 23 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU B 25 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 22 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB3, first strand: chain 'B' and resid 282 through 283 removed outlier: 3.611A pdb=" N ALA B 282 " --> pdb=" O ALA B 499 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AB5, first strand: chain 'B' and resid 575 through 581 removed outlier: 3.565A pdb=" N GLY B 771 " --> pdb=" O SER B 652 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE B 653 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER B 726 " --> pdb=" O PHE B 653 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLY B 655 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 739 through 740 Processing sheet with id=AB7, first strand: chain 'B' and resid 750 through 751 Processing sheet with id=AB8, first strand: chain 'B' and resid 983 through 984 Processing sheet with id=AB9, first strand: chain 'B' and resid 986 through 989 removed outlier: 6.708A pdb=" N GLN B 994 " --> pdb=" O ILE B 988 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1083 through 1085 removed outlier: 3.513A pdb=" N ILE B1131 " --> pdb=" O ASP B1092 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B1128 " --> pdb=" O LEU B1150 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE B1152 " --> pdb=" O VAL B1128 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B1130 " --> pdb=" O ILE B1152 " (cutoff:3.500A) 939 hydrogen bonds defined for protein. 2676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5111 1.33 - 1.45: 4087 1.45 - 1.57: 11124 1.57 - 1.69: 81 1.69 - 1.81: 108 Bond restraints: 20511 Sorted by residual: bond pdb=" O3' DA D 31 " pdb=" P DG D 32 " ideal model delta sigma weight residual 1.607 1.518 0.089 1.20e-02 6.94e+03 5.44e+01 bond pdb=" O3' DT C 37 " pdb=" P DC C 38 " ideal model delta sigma weight residual 1.607 1.680 -0.073 1.20e-02 6.94e+03 3.69e+01 bond pdb=" C1' DT C 27 " pdb=" N1 DT C 27 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.46e+01 bond pdb=" O3' DT C 35 " pdb=" P DA C 36 " ideal model delta sigma weight residual 1.607 1.537 0.070 1.20e-02 6.94e+03 3.36e+01 bond pdb=" O3' DA C 36 " pdb=" P DT C 37 " ideal model delta sigma weight residual 1.607 1.540 0.067 1.20e-02 6.94e+03 3.10e+01 ... (remaining 20506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 27422 2.41 - 4.83: 375 4.83 - 7.24: 62 7.24 - 9.65: 11 9.65 - 12.06: 6 Bond angle restraints: 27876 Sorted by residual: angle pdb=" N ALA A 181 " pdb=" CA ALA A 181 " pdb=" C ALA A 181 " ideal model delta sigma weight residual 113.17 101.75 11.42 1.26e+00 6.30e-01 8.21e+01 angle pdb=" N PRO A 618 " pdb=" CA PRO A 618 " pdb=" CB PRO A 618 " ideal model delta sigma weight residual 103.25 110.74 -7.49 1.05e+00 9.07e-01 5.08e+01 angle pdb=" N ALA A 181 " pdb=" CA ALA A 181 " pdb=" CB ALA A 181 " ideal model delta sigma weight residual 110.49 120.62 -10.13 1.48e+00 4.57e-01 4.68e+01 angle pdb=" N PRO A 866 " pdb=" CA PRO A 866 " pdb=" CB PRO A 866 " ideal model delta sigma weight residual 103.38 110.40 -7.02 1.05e+00 9.07e-01 4.46e+01 angle pdb=" N PRO B 618 " pdb=" CA PRO B 618 " pdb=" CB PRO B 618 " ideal model delta sigma weight residual 103.00 110.10 -7.10 1.10e+00 8.26e-01 4.16e+01 ... (remaining 27871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 11852 34.85 - 69.70: 432 69.70 - 104.55: 40 104.55 - 139.40: 3 139.40 - 174.25: 3 Dihedral angle restraints: 12330 sinusoidal: 5439 harmonic: 6891 Sorted by residual: dihedral pdb=" C2' ADP B1201 " pdb=" C1' ADP B1201 " pdb=" N9 ADP B1201 " pdb=" C4 ADP B1201 " ideal model delta sinusoidal sigma weight residual 91.55 -82.70 174.25 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP B1201 " pdb=" O3A ADP B1201 " pdb=" PB ADP B1201 " pdb=" PA ADP B1201 " ideal model delta sinusoidal sigma weight residual -60.00 74.83 -134.83 1 2.00e+01 2.50e-03 4.09e+01 dihedral pdb=" O2A ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PA ADP A1201 " pdb=" PB ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 55.36 -115.36 1 2.00e+01 2.50e-03 3.43e+01 ... (remaining 12327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2608 0.065 - 0.129: 376 0.129 - 0.194: 38 0.194 - 0.259: 7 0.259 - 0.324: 4 Chirality restraints: 3033 Sorted by residual: chirality pdb=" C3' DA C 31 " pdb=" C4' DA C 31 " pdb=" O3' DA C 31 " pdb=" C2' DA C 31 " both_signs ideal model delta sigma weight residual False -2.73 -2.41 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA SER B 459 " pdb=" N SER B 459 " pdb=" C SER B 459 " pdb=" CB SER B 459 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ILE A 176 " pdb=" N ILE A 176 " pdb=" C ILE A 176 " pdb=" CB ILE A 176 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3030 not shown) Planarity restraints: 3439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT C 35 " 0.007 2.00e-02 2.50e+03 2.59e-02 1.67e+01 pdb=" N1 DT C 35 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DT C 35 " 0.007 2.00e-02 2.50e+03 pdb=" O2 DT C 35 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DT C 35 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DT C 35 " -0.065 2.00e-02 2.50e+03 pdb=" O4 DT C 35 " 0.036 2.00e-02 2.50e+03 pdb=" C5 DT C 35 " -0.020 2.00e-02 2.50e+03 pdb=" C7 DT C 35 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DT C 35 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 36 " -0.028 2.00e-02 2.50e+03 2.05e-02 1.16e+01 pdb=" N9 DA D 36 " 0.014 2.00e-02 2.50e+03 pdb=" C8 DA D 36 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA D 36 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DA D 36 " 0.052 2.00e-02 2.50e+03 pdb=" C6 DA D 36 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA D 36 " -0.028 2.00e-02 2.50e+03 pdb=" N1 DA D 36 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DA D 36 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA D 36 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA D 36 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 459 " 0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO A 460 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " 0.044 5.00e-02 4.00e+02 ... (remaining 3436 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3074 2.75 - 3.29: 19971 3.29 - 3.83: 34452 3.83 - 4.36: 41342 4.36 - 4.90: 69158 Nonbonded interactions: 167997 Sorted by model distance: nonbonded pdb=" O LEU A1115 " pdb=" NE2 GLN A1119 " model vdw 2.214 3.120 nonbonded pdb=" CD2 LEU A 659 " pdb=" OP1 DG C 32 " model vdw 2.216 3.460 nonbonded pdb=" OG1 THR A 227 " pdb=" OP1 DT C 37 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR A 945 " pdb=" O GLY A 970 " model vdw 2.233 3.040 nonbonded pdb=" O GLU B 261 " pdb=" N SER B 264 " model vdw 2.233 3.120 ... (remaining 167992 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' and (resid 1 through 618 or resid 626 through 1177 or resid 1201)) selection = (chain 'B' and (resid 1 through 461 or (resid 462 through 464 and (name N or nam \ e CA or name C or name O or name CB )) or resid 465 through 865 or (resid 866 an \ d (name N or name CA or name C or name O or name CB )) or resid 867 through 1201 \ )) } ncs_group { reference = (chain 'C' and resid 28 through 39) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.020 Process input model: 19.620 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 0.089 20511 Z= 0.319 Angle : 0.732 12.064 27876 Z= 0.439 Chirality : 0.048 0.324 3033 Planarity : 0.004 0.084 3439 Dihedral : 17.461 174.248 7864 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.38 % Favored : 94.19 % Rotamer: Outliers : 1.02 % Allowed : 0.88 % Favored : 98.10 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2342 helix: 1.26 (0.16), residues: 1112 sheet: -0.72 (0.33), residues: 265 loop : -1.80 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.016 0.002 TYR B 938 PHE 0.024 0.002 PHE B 641 TRP 0.036 0.002 TRP A1126 HIS 0.009 0.001 HIS B 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.32 (20511) covalent geometry : angle 0.73211 / 0.44 (27876) hydrogen bonds : bond 0.13692 / 9.06 ( 939) hydrogen bonds : angle 5.93864 / 4.17 ( 2676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8770 (m-30) cc_final: 0.8425 (m-30) REVERT: A 671 TYR cc_start: 0.7567 (t80) cc_final: 0.7242 (t80) REVERT: A 741 MET cc_start: 0.6969 (ttm) cc_final: 0.5421 (mpt) REVERT: A 784 ASN cc_start: 0.8713 (m110) cc_final: 0.7949 (p0) REVERT: A 788 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8280 (mtm-85) REVERT: A 840 TYR cc_start: 0.8709 (t80) cc_final: 0.8241 (t80) REVERT: A 942 ARG cc_start: 0.8041 (ttt180) cc_final: 0.7771 (ttt180) REVERT: A 1014 MET cc_start: 0.0782 (ptt) cc_final: -0.0430 (mpt) REVERT: A 1143 MET cc_start: 0.6440 (mmm) cc_final: 0.5318 (mpt) REVERT: B 263 ASP cc_start: 0.8469 (p0) cc_final: 0.8167 (p0) REVERT: B 276 GLU cc_start: 0.8642 (tp30) cc_final: 0.8441 (mm-30) REVERT: B 459 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7306 (p) REVERT: B 612 LYS cc_start: 0.9076 (tppt) cc_final: 0.8829 (ttmm) REVERT: B 922 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8074 (mmp80) REVERT: B 943 TRP cc_start: 0.8689 (m100) cc_final: 0.7609 (m-90) REVERT: B 977 GLU cc_start: 0.7944 (pm20) cc_final: 0.7681 (pm20) REVERT: B 979 LEU cc_start: 0.9295 (mt) cc_final: 0.9046 (mm) REVERT: B 992 ASN cc_start: 0.8907 (t0) cc_final: 0.8671 (t160) REVERT: B 1034 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 1143 MET cc_start: 0.7548 (mpp) cc_final: 0.7348 (mpp) outliers start: 21 outliers final: 7 residues processed: 239 average time/residue: 0.6069 time to fit residues: 162.2525 Evaluate side-chains 147 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain B residue 1172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.0980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 657 GLN ** B1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1168 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.128238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.077698 restraints weight = 34200.757| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.85 r_work: 0.2823 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20511 Z= 0.199 Angle : 0.639 9.705 27876 Z= 0.339 Chirality : 0.045 0.249 3033 Planarity : 0.005 0.062 3439 Dihedral : 16.985 175.906 3141 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.00 % Favored : 94.88 % Rotamer: Outliers : 1.70 % Allowed : 7.59 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2342 helix: 1.46 (0.16), residues: 1117 sheet: -0.53 (0.33), residues: 254 loop : -1.68 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 762 TYR 0.019 0.002 TYR A1048 PHE 0.030 0.002 PHE B 641 TRP 0.017 0.001 TRP A1126 HIS 0.006 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (20511) covalent geometry : angle 0.63889 / 0.34 (27876) hydrogen bonds : bond 0.05064 / 3.45 ( 939) hydrogen bonds : angle 4.90666 / 3.48 ( 2676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8725 (m-30) cc_final: 0.8282 (m-30) REVERT: A 671 TYR cc_start: 0.7543 (t80) cc_final: 0.7102 (t80) REVERT: A 741 MET cc_start: 0.7163 (ttm) cc_final: 0.5408 (mpt) REVERT: A 788 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8375 (mtm-85) REVERT: A 922 ARG cc_start: 0.7745 (tpp-160) cc_final: 0.7344 (tmm160) REVERT: A 1014 MET cc_start: 0.1026 (ptt) cc_final: -0.0412 (mpt) REVERT: A 1143 MET cc_start: 0.6558 (mmm) cc_final: 0.5467 (mpt) REVERT: B 139 ASN cc_start: 0.7362 (t0) cc_final: 0.6708 (t0) REVERT: B 140 GLU cc_start: 0.8374 (pm20) cc_final: 0.8013 (pm20) REVERT: B 141 PHE cc_start: 0.8924 (m-80) cc_final: 0.8360 (m-80) REVERT: B 263 ASP cc_start: 0.8266 (p0) cc_final: 0.8019 (p0) REVERT: B 276 GLU cc_start: 0.8442 (tp30) cc_final: 0.8223 (mm-30) REVERT: B 582 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8605 (pp) REVERT: B 586 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7680 (p90) REVERT: B 616 CYS cc_start: 0.8895 (m) cc_final: 0.8657 (p) REVERT: B 922 ARG cc_start: 0.8355 (mmm160) cc_final: 0.7947 (mmp80) REVERT: B 943 TRP cc_start: 0.8580 (m100) cc_final: 0.7488 (m-90) REVERT: B 977 GLU cc_start: 0.8067 (pm20) cc_final: 0.7775 (pm20) REVERT: B 979 LEU cc_start: 0.9167 (mt) cc_final: 0.8926 (mm) REVERT: B 986 LYS cc_start: 0.8420 (tttt) cc_final: 0.8101 (tmmm) REVERT: B 992 ASN cc_start: 0.8919 (t0) cc_final: 0.8539 (t160) REVERT: B 1034 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7405 (tm-30) outliers start: 35 outliers final: 12 residues processed: 172 average time/residue: 0.6251 time to fit residues: 121.6076 Evaluate side-chains 143 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 868 ASN Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 990 HIS Chi-restraints excluded: chain B residue 1064 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 158 optimal weight: 0.5980 chunk 55 optimal weight: 0.0470 chunk 216 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 225 optimal weight: 20.0000 chunk 147 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 GLN A 128 ASN A 700 ASN A 707 GLN A 779 HIS A1063 ASN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.128742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078053 restraints weight = 34292.847| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.92 r_work: 0.2841 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20511 Z= 0.180 Angle : 0.594 9.760 27876 Z= 0.314 Chirality : 0.043 0.244 3033 Planarity : 0.004 0.059 3439 Dihedral : 16.803 178.124 3132 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 1.75 % Allowed : 10.55 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 2342 helix: 1.60 (0.16), residues: 1119 sheet: -0.53 (0.34), residues: 254 loop : -1.63 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 632 TYR 0.018 0.002 TYR A1046 PHE 0.029 0.001 PHE B 641 TRP 0.030 0.002 TRP A 897 HIS 0.007 0.001 HIS B 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (20511) covalent geometry : angle 0.59438 / 0.31 (27876) hydrogen bonds : bond 0.04686 / 3.20 ( 939) hydrogen bonds : angle 4.66380 / 3.31 ( 2676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8788 (mm-30) REVERT: A 271 GLU cc_start: 0.8315 (mp0) cc_final: 0.8095 (mm-30) REVERT: A 533 ASP cc_start: 0.8691 (m-30) cc_final: 0.8242 (m-30) REVERT: A 638 PHE cc_start: 0.8558 (m-80) cc_final: 0.8283 (m-80) REVERT: A 671 TYR cc_start: 0.7221 (t80) cc_final: 0.6829 (t80) REVERT: A 741 MET cc_start: 0.7254 (ttm) cc_final: 0.5482 (mpt) REVERT: A 765 HIS cc_start: 0.6886 (p90) cc_final: 0.6610 (p90) REVERT: A 788 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8472 (mtm-85) REVERT: A 922 ARG cc_start: 0.7755 (tpp-160) cc_final: 0.7328 (tmm160) REVERT: A 1014 MET cc_start: 0.1032 (ptt) cc_final: -0.0744 (mpt) REVERT: A 1143 MET cc_start: 0.6288 (mmm) cc_final: 0.5300 (mpt) REVERT: B 139 ASN cc_start: 0.7376 (t0) cc_final: 0.6916 (t0) REVERT: B 141 PHE cc_start: 0.8904 (m-80) cc_final: 0.8482 (m-80) REVERT: B 276 GLU cc_start: 0.8486 (tp30) cc_final: 0.8250 (mm-30) REVERT: B 313 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7218 (p90) REVERT: B 582 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8597 (pp) REVERT: B 586 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7887 (p90) REVERT: B 616 CYS cc_start: 0.8922 (m) cc_final: 0.8712 (p) REVERT: B 726 SER cc_start: 0.9539 (t) cc_final: 0.9301 (m) REVERT: B 943 TRP cc_start: 0.8584 (m100) cc_final: 0.7391 (m-90) REVERT: B 977 GLU cc_start: 0.8094 (pm20) cc_final: 0.7800 (pm20) REVERT: B 979 LEU cc_start: 0.9161 (mt) cc_final: 0.8914 (mm) REVERT: B 986 LYS cc_start: 0.8390 (tttt) cc_final: 0.8072 (tmmm) REVERT: B 992 ASN cc_start: 0.8956 (t0) cc_final: 0.8532 (t160) REVERT: B 1014 MET cc_start: 0.6834 (ttm) cc_final: 0.6555 (ttm) REVERT: B 1034 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7394 (tm-30) outliers start: 36 outliers final: 13 residues processed: 165 average time/residue: 0.5871 time to fit residues: 110.4204 Evaluate side-chains 143 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 990 HIS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 990 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 164 optimal weight: 0.3980 chunk 147 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 HIS ** B1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 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 = 0.3844 r_free = 0.3844 target = 0.130283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.079514 restraints weight = 34098.291| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.92 r_work: 0.2871 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20511 Z= 0.127 Angle : 0.559 9.207 27876 Z= 0.294 Chirality : 0.041 0.226 3033 Planarity : 0.004 0.058 3439 Dihedral : 16.622 179.469 3132 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 2.04 % Allowed : 11.04 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 2342 helix: 1.71 (0.16), residues: 1125 sheet: -0.37 (0.34), residues: 251 loop : -1.59 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 633 TYR 0.018 0.001 TYR A1046 PHE 0.025 0.001 PHE B 641 TRP 0.014 0.001 TRP A 897 HIS 0.006 0.001 HIS B 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (20511) covalent geometry : angle 0.55907 / 0.29 (27876) hydrogen bonds : bond 0.04234 / 2.89 ( 939) hydrogen bonds : angle 4.47846 / 3.19 ( 2676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8637 (m-30) cc_final: 0.8210 (m-30) REVERT: A 638 PHE cc_start: 0.8559 (m-80) cc_final: 0.8241 (m-80) REVERT: A 698 SER cc_start: 0.8125 (t) cc_final: 0.7755 (p) REVERT: A 741 MET cc_start: 0.7244 (ttm) cc_final: 0.5423 (mpt) REVERT: A 788 ARG cc_start: 0.8753 (mtm-85) cc_final: 0.8482 (mtm-85) REVERT: A 922 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.7379 (tmm160) REVERT: A 1014 MET cc_start: 0.0730 (ptt) cc_final: -0.1161 (mpt) REVERT: A 1143 MET cc_start: 0.6485 (mmm) cc_final: 0.5367 (mpt) REVERT: B 141 PHE cc_start: 0.8905 (m-80) cc_final: 0.8511 (m-80) REVERT: B 276 GLU cc_start: 0.8449 (tp30) cc_final: 0.8227 (mm-30) REVERT: B 313 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7317 (p90) REVERT: B 582 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8589 (pp) REVERT: B 616 CYS cc_start: 0.8916 (m) cc_final: 0.8680 (p) REVERT: B 726 SER cc_start: 0.9551 (t) cc_final: 0.9310 (m) REVERT: B 740 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8251 (mm-30) REVERT: B 943 TRP cc_start: 0.8591 (m100) cc_final: 0.7331 (m-90) REVERT: B 977 GLU cc_start: 0.8112 (pm20) cc_final: 0.7797 (pm20) REVERT: B 979 LEU cc_start: 0.9170 (mt) cc_final: 0.8922 (mm) REVERT: B 986 LYS cc_start: 0.8367 (tttt) cc_final: 0.8067 (tmmm) REVERT: B 992 ASN cc_start: 0.8962 (t0) cc_final: 0.8518 (t160) REVERT: B 1014 MET cc_start: 0.6599 (ttm) cc_final: 0.6371 (ttm) REVERT: B 1034 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7253 (tm-30) outliers start: 42 outliers final: 12 residues processed: 165 average time/residue: 0.5368 time to fit residues: 101.0544 Evaluate side-chains 140 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 990 HIS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 990 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 135 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 98 optimal weight: 0.1980 chunk 11 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 707 GLN A 871 GLN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN B1058 GLN ** B1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.075673 restraints weight = 34362.826| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.96 r_work: 0.2797 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 20511 Z= 0.277 Angle : 0.642 10.754 27876 Z= 0.335 Chirality : 0.045 0.274 3033 Planarity : 0.005 0.097 3439 Dihedral : 16.532 178.087 3131 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.45 % Rotamer: Outliers : 2.33 % Allowed : 12.21 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2342 helix: 1.65 (0.16), residues: 1128 sheet: -0.51 (0.34), residues: 253 loop : -1.61 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 632 TYR 0.029 0.002 TYR A 671 PHE 0.037 0.002 PHE B 641 TRP 0.016 0.001 TRP B 943 HIS 0.006 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.28 (20511) covalent geometry : angle 0.64174 / 0.34 (27876) hydrogen bonds : bond 0.04860 / 3.32 ( 939) hydrogen bonds : angle 4.58775 / 3.27 ( 2676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8681 (m-30) cc_final: 0.8271 (m-30) REVERT: A 638 PHE cc_start: 0.8564 (m-80) cc_final: 0.8253 (m-80) REVERT: A 698 SER cc_start: 0.8133 (t) cc_final: 0.7746 (p) REVERT: A 741 MET cc_start: 0.7229 (ttm) cc_final: 0.5325 (mpt) REVERT: A 788 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8476 (mtm-85) REVERT: A 922 ARG cc_start: 0.7857 (tpp-160) cc_final: 0.7366 (tmm160) REVERT: A 1003 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: A 1143 MET cc_start: 0.6391 (mmm) cc_final: 0.5495 (mpt) REVERT: B 139 ASN cc_start: 0.7486 (t0) cc_final: 0.7033 (t0) REVERT: B 141 PHE cc_start: 0.8937 (m-80) cc_final: 0.8500 (m-80) REVERT: B 271 GLU cc_start: 0.8457 (tt0) cc_final: 0.7748 (tp30) REVERT: B 276 GLU cc_start: 0.8544 (tp30) cc_final: 0.8323 (mm-30) REVERT: B 313 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7449 (p90) REVERT: B 582 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8579 (pp) REVERT: B 726 SER cc_start: 0.9528 (t) cc_final: 0.9235 (m) REVERT: B 740 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8358 (mm-30) REVERT: B 883 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7699 (p) REVERT: B 943 TRP cc_start: 0.8652 (m100) cc_final: 0.8331 (m-90) REVERT: B 977 GLU cc_start: 0.8143 (pm20) cc_final: 0.7871 (pm20) REVERT: B 979 LEU cc_start: 0.9161 (mt) cc_final: 0.8886 (mm) REVERT: B 986 LYS cc_start: 0.8406 (tttt) cc_final: 0.8149 (tmmm) REVERT: B 992 ASN cc_start: 0.8954 (t0) cc_final: 0.8514 (t160) outliers start: 48 outliers final: 16 residues processed: 165 average time/residue: 0.5433 time to fit residues: 102.8565 Evaluate side-chains 146 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 953 ASP Chi-restraints excluded: chain A residue 990 HIS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 990 HIS Chi-restraints excluded: chain B residue 1152 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.0670 chunk 203 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 HIS A 871 GLN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 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 = 0.3878 r_free = 0.3878 target = 0.131244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081184 restraints weight = 33862.015| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.86 r_work: 0.2906 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20511 Z= 0.126 Angle : 0.570 9.681 27876 Z= 0.297 Chirality : 0.042 0.320 3033 Planarity : 0.004 0.070 3439 Dihedral : 16.416 178.637 3130 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 1.80 % Allowed : 13.57 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 2342 helix: 1.79 (0.16), residues: 1126 sheet: -0.32 (0.34), residues: 252 loop : -1.51 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 632 TYR 0.021 0.001 TYR A1046 PHE 0.025 0.001 PHE B 641 TRP 0.011 0.001 TRP A1126 HIS 0.008 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (20511) covalent geometry : angle 0.57012 / 0.30 (27876) hydrogen bonds : bond 0.04168 / 2.86 ( 939) hydrogen bonds : angle 4.42192 / 3.15 ( 2676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8624 (m-30) cc_final: 0.8259 (m-30) REVERT: A 638 PHE cc_start: 0.8650 (m-80) cc_final: 0.8349 (m-80) REVERT: A 698 SER cc_start: 0.8199 (t) cc_final: 0.7822 (p) REVERT: A 741 MET cc_start: 0.7072 (ttm) cc_final: 0.5286 (mpt) REVERT: A 788 ARG cc_start: 0.8819 (mtm-85) cc_final: 0.8565 (mtm-85) REVERT: A 852 ASN cc_start: 0.8277 (m-40) cc_final: 0.8076 (m110) REVERT: A 922 ARG cc_start: 0.7841 (tpp-160) cc_final: 0.7426 (tmm160) REVERT: A 1003 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: A 1014 MET cc_start: 0.0367 (ptt) cc_final: -0.1267 (mpt) REVERT: A 1143 MET cc_start: 0.6281 (mmm) cc_final: 0.5317 (mpt) REVERT: B 141 PHE cc_start: 0.8924 (m-80) cc_final: 0.8507 (m-80) REVERT: B 253 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8740 (tppt) REVERT: B 276 GLU cc_start: 0.8569 (tp30) cc_final: 0.8356 (mm-30) REVERT: B 313 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7549 (p90) REVERT: B 582 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8572 (pp) REVERT: B 616 CYS cc_start: 0.8941 (m) cc_final: 0.8726 (p) REVERT: B 726 SER cc_start: 0.9504 (t) cc_final: 0.9238 (m) REVERT: B 922 ARG cc_start: 0.8397 (mmm160) cc_final: 0.7957 (mmp80) REVERT: B 943 TRP cc_start: 0.8705 (m100) cc_final: 0.8419 (m-90) REVERT: B 977 GLU cc_start: 0.8135 (pm20) cc_final: 0.7862 (pm20) REVERT: B 979 LEU cc_start: 0.9234 (mt) cc_final: 0.8972 (mm) REVERT: B 986 LYS cc_start: 0.8481 (tttt) cc_final: 0.8221 (tmmm) REVERT: B 992 ASN cc_start: 0.8993 (t0) cc_final: 0.8532 (t160) outliers start: 37 outliers final: 15 residues processed: 160 average time/residue: 0.6196 time to fit residues: 113.7856 Evaluate side-chains 142 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 990 HIS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 990 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 41 optimal weight: 0.5980 chunk 85 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.3867 > 50:) chunk 13 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 230 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 34 optimal weight: 0.0040 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 HIS A 871 GLN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN B 948 HIS ** B1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.131530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.080784 restraints weight = 34193.126| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.91 r_work: 0.2904 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20511 Z= 0.130 Angle : 0.571 10.892 27876 Z= 0.297 Chirality : 0.042 0.342 3033 Planarity : 0.004 0.063 3439 Dihedral : 16.357 179.073 3130 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 1.51 % Allowed : 14.30 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2342 helix: 1.84 (0.16), residues: 1126 sheet: -0.28 (0.34), residues: 251 loop : -1.45 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 632 TYR 0.020 0.001 TYR A1046 PHE 0.024 0.001 PHE B 641 TRP 0.012 0.001 TRP A 934 HIS 0.006 0.001 HIS B 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (20511) covalent geometry : angle 0.57106 / 0.30 (27876) hydrogen bonds : bond 0.04098 / 2.81 ( 939) hydrogen bonds : angle 4.35560 / 3.11 ( 2676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8642 (m-30) cc_final: 0.8269 (m-30) REVERT: A 698 SER cc_start: 0.8178 (t) cc_final: 0.7808 (p) REVERT: A 741 MET cc_start: 0.7116 (ttm) cc_final: 0.5302 (mpt) REVERT: A 788 ARG cc_start: 0.8803 (mtm-85) cc_final: 0.8552 (mtm-85) REVERT: A 858 MET cc_start: 0.7573 (tmt) cc_final: 0.7117 (tmm) REVERT: A 922 ARG cc_start: 0.7802 (tpp-160) cc_final: 0.7431 (tmm160) REVERT: A 1003 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: A 1014 MET cc_start: 0.0301 (ptt) cc_final: -0.1246 (mpt) REVERT: A 1143 MET cc_start: 0.6344 (mmm) cc_final: 0.5254 (mpt) REVERT: B 66 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8155 (mp10) REVERT: B 141 PHE cc_start: 0.8927 (m-80) cc_final: 0.8535 (m-80) REVERT: B 253 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8720 (tppt) REVERT: B 276 GLU cc_start: 0.8573 (tp30) cc_final: 0.8346 (mm-30) REVERT: B 313 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7451 (p90) REVERT: B 582 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8558 (pp) REVERT: B 616 CYS cc_start: 0.8945 (m) cc_final: 0.8741 (p) REVERT: B 726 SER cc_start: 0.9507 (t) cc_final: 0.9239 (m) REVERT: B 943 TRP cc_start: 0.8703 (m100) cc_final: 0.8416 (m-90) REVERT: B 977 GLU cc_start: 0.8151 (pm20) cc_final: 0.7869 (pm20) REVERT: B 979 LEU cc_start: 0.9224 (mt) cc_final: 0.8957 (mm) REVERT: B 986 LYS cc_start: 0.8473 (tttt) cc_final: 0.8216 (tmmm) REVERT: B 992 ASN cc_start: 0.9006 (t0) cc_final: 0.8533 (t160) outliers start: 31 outliers final: 16 residues processed: 148 average time/residue: 0.5546 time to fit residues: 94.0516 Evaluate side-chains 142 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 990 HIS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 948 HIS Chi-restraints excluded: chain B residue 990 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 175 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 160 optimal weight: 0.0070 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 ASN ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 HIS ** B1121 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 = 0.3887 r_free = 0.3887 target = 0.132007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.081690 restraints weight = 34088.562| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.88 r_work: 0.2918 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20511 Z= 0.120 Angle : 0.569 10.711 27876 Z= 0.294 Chirality : 0.042 0.330 3033 Planarity : 0.004 0.065 3439 Dihedral : 16.302 179.305 3130 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 1.56 % Allowed : 14.45 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2342 helix: 1.85 (0.15), residues: 1126 sheet: -0.23 (0.34), residues: 251 loop : -1.44 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 632 TYR 0.021 0.001 TYR A1046 PHE 0.028 0.001 PHE A 638 TRP 0.011 0.001 TRP A1065 HIS 0.020 0.001 HIS B 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (20511) covalent geometry : angle 0.56868 / 0.29 (27876) hydrogen bonds : bond 0.03974 / 2.73 ( 939) hydrogen bonds : angle 4.32570 / 3.09 ( 2676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8622 (m-30) cc_final: 0.8250 (m-30) REVERT: A 698 SER cc_start: 0.8172 (t) cc_final: 0.7807 (p) REVERT: A 741 MET cc_start: 0.7152 (ttm) cc_final: 0.5355 (mpt) REVERT: A 788 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8555 (mtm-85) REVERT: A 865 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7427 (ppp) REVERT: A 922 ARG cc_start: 0.7790 (tpp-160) cc_final: 0.7440 (tmm160) REVERT: A 948 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.7875 (p90) REVERT: A 1003 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: A 1014 MET cc_start: 0.0261 (ptt) cc_final: -0.1246 (mpt) REVERT: A 1143 MET cc_start: 0.6339 (mmm) cc_final: 0.5213 (mpt) REVERT: B 66 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8160 (mp10) REVERT: B 141 PHE cc_start: 0.8950 (m-80) cc_final: 0.8545 (m-80) REVERT: B 253 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8701 (tppt) REVERT: B 276 GLU cc_start: 0.8569 (tp30) cc_final: 0.8342 (mm-30) REVERT: B 313 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7469 (p90) REVERT: B 582 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8559 (pp) REVERT: B 616 CYS cc_start: 0.8944 (m) cc_final: 0.8725 (p) REVERT: B 726 SER cc_start: 0.9506 (t) cc_final: 0.9241 (m) REVERT: B 922 ARG cc_start: 0.8127 (mmt-90) cc_final: 0.7572 (mmp80) REVERT: B 943 TRP cc_start: 0.8731 (m100) cc_final: 0.8424 (m-90) REVERT: B 977 GLU cc_start: 0.8148 (pm20) cc_final: 0.7856 (pm20) REVERT: B 979 LEU cc_start: 0.9217 (mt) cc_final: 0.8945 (mm) REVERT: B 986 LYS cc_start: 0.8490 (tttt) cc_final: 0.8239 (tmmm) REVERT: B 992 ASN cc_start: 0.9010 (t0) cc_final: 0.8539 (t160) outliers start: 32 outliers final: 17 residues processed: 154 average time/residue: 0.6421 time to fit residues: 112.6382 Evaluate side-chains 149 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 990 HIS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 948 HIS Chi-restraints excluded: chain B residue 990 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 49 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 HIS A 852 ASN ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 HIS ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.129619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.079469 restraints weight = 34142.619| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.86 r_work: 0.2872 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20511 Z= 0.218 Angle : 0.612 11.216 27876 Z= 0.316 Chirality : 0.044 0.356 3033 Planarity : 0.004 0.066 3439 Dihedral : 16.279 178.062 3130 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 1.41 % Allowed : 14.93 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2342 helix: 1.82 (0.15), residues: 1127 sheet: -0.43 (0.33), residues: 262 loop : -1.46 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 632 TYR 0.022 0.002 TYR A1046 PHE 0.032 0.002 PHE B 641 TRP 0.015 0.001 TRP A 934 HIS 0.023 0.001 HIS B 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (20511) covalent geometry : angle 0.61179 / 0.32 (27876) hydrogen bonds : bond 0.04364 / 2.99 ( 939) hydrogen bonds : angle 4.41328 / 3.15 ( 2676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8672 (m-30) cc_final: 0.8305 (m-30) REVERT: A 698 SER cc_start: 0.8222 (t) cc_final: 0.7854 (p) REVERT: A 741 MET cc_start: 0.7107 (ttm) cc_final: 0.5251 (mpt) REVERT: A 788 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8554 (mtm-85) REVERT: A 922 ARG cc_start: 0.7871 (tpp-160) cc_final: 0.7466 (tmm160) REVERT: A 948 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.7989 (p90) REVERT: A 1003 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: A 1014 MET cc_start: 0.0420 (ptt) cc_final: -0.1074 (mpt) REVERT: A 1143 MET cc_start: 0.6362 (mmm) cc_final: 0.5327 (mpt) REVERT: B 66 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8179 (mp10) REVERT: B 141 PHE cc_start: 0.8941 (m-80) cc_final: 0.8538 (m-80) REVERT: B 173 LEU cc_start: 0.8744 (tp) cc_final: 0.8395 (tm) REVERT: B 276 GLU cc_start: 0.8613 (tp30) cc_final: 0.8412 (mm-30) REVERT: B 313 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7571 (p90) REVERT: B 582 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8569 (pp) REVERT: B 616 CYS cc_start: 0.8962 (m) cc_final: 0.8728 (p) REVERT: B 726 SER cc_start: 0.9496 (t) cc_final: 0.9177 (m) REVERT: B 922 ARG cc_start: 0.8050 (mmt-90) cc_final: 0.7591 (mmp80) REVERT: B 943 TRP cc_start: 0.8777 (m100) cc_final: 0.8466 (m-90) REVERT: B 977 GLU cc_start: 0.8129 (pm20) cc_final: 0.7872 (pm20) REVERT: B 979 LEU cc_start: 0.9237 (mt) cc_final: 0.8948 (mm) REVERT: B 986 LYS cc_start: 0.8432 (tttt) cc_final: 0.8175 (tmmm) REVERT: B 992 ASN cc_start: 0.8995 (t0) cc_final: 0.8532 (t160) outliers start: 29 outliers final: 19 residues processed: 151 average time/residue: 0.5663 time to fit residues: 98.1098 Evaluate side-chains 149 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 990 HIS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain B residue 948 HIS Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 990 HIS Chi-restraints excluded: chain B residue 1152 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 85 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 232 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 ASN ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 948 HIS ** B1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.130250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079303 restraints weight = 34214.018| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.90 r_work: 0.2895 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20511 Z= 0.185 Angle : 0.609 11.711 27876 Z= 0.313 Chirality : 0.043 0.358 3033 Planarity : 0.004 0.104 3439 Dihedral : 16.247 177.360 3130 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 1.46 % Allowed : 14.93 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2342 helix: 1.81 (0.15), residues: 1127 sheet: -0.41 (0.34), residues: 262 loop : -1.48 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 585 TYR 0.023 0.001 TYR A1046 PHE 0.029 0.001 PHE B 641 TRP 0.014 0.001 TRP B 943 HIS 0.022 0.001 HIS B 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (20511) covalent geometry : angle 0.60868 / 0.31 (27876) hydrogen bonds : bond 0.04308 / 2.95 ( 939) hydrogen bonds : angle 4.40213 / 3.14 ( 2676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4684 Ramachandran restraints generated. 2342 Oldfield, 0 Emsley, 2342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8659 (m-30) cc_final: 0.8303 (m-30) REVERT: A 698 SER cc_start: 0.8226 (t) cc_final: 0.7867 (p) REVERT: A 741 MET cc_start: 0.7144 (ttm) cc_final: 0.5326 (mpt) REVERT: A 788 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8550 (mtm-85) REVERT: A 858 MET cc_start: 0.7564 (tmt) cc_final: 0.7154 (tmm) REVERT: A 865 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7383 (ppp) REVERT: A 922 ARG cc_start: 0.7871 (tpp-160) cc_final: 0.7482 (tmm160) REVERT: A 948 HIS cc_start: 0.8467 (OUTLIER) cc_final: 0.7998 (p90) REVERT: A 1003 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: A 1014 MET cc_start: 0.0321 (ptt) cc_final: -0.1268 (mpt) REVERT: A 1143 MET cc_start: 0.6370 (mmm) cc_final: 0.5331 (mpt) REVERT: B 66 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8164 (mp10) REVERT: B 141 PHE cc_start: 0.8924 (m-80) cc_final: 0.8510 (m-80) REVERT: B 173 LEU cc_start: 0.8733 (tp) cc_final: 0.8367 (tm) REVERT: B 253 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8730 (tppt) REVERT: B 271 GLU cc_start: 0.8440 (tt0) cc_final: 0.8224 (pt0) REVERT: B 276 GLU cc_start: 0.8617 (tp30) cc_final: 0.8417 (mm-30) REVERT: B 313 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7575 (p90) REVERT: B 344 ARG cc_start: 0.7899 (ptm-80) cc_final: 0.7522 (ppt170) REVERT: B 582 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8557 (pp) REVERT: B 616 CYS cc_start: 0.8977 (m) cc_final: 0.8741 (p) REVERT: B 726 SER cc_start: 0.9494 (t) cc_final: 0.9175 (m) REVERT: B 943 TRP cc_start: 0.8792 (m100) cc_final: 0.8440 (m-90) REVERT: B 948 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7499 (p-80) REVERT: B 977 GLU cc_start: 0.8127 (pm20) cc_final: 0.7868 (pm20) REVERT: B 979 LEU cc_start: 0.9251 (mt) cc_final: 0.8956 (mm) REVERT: B 992 ASN cc_start: 0.8996 (t0) cc_final: 0.8527 (t160) outliers start: 30 outliers final: 18 residues processed: 148 average time/residue: 0.6543 time to fit residues: 110.3957 Evaluate side-chains 149 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 990 HIS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 783 SER Chi-restraints excluded: chain B residue 948 HIS Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 990 HIS Chi-restraints excluded: chain B residue 1152 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 83 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 ASN ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 HIS ** B1121 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 = 0.3873 r_free = 0.3873 target = 0.131075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080119 restraints weight = 34236.416| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.90 r_work: 0.2892 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20511 Z= 0.138 Angle : 0.591 11.988 27876 Z= 0.304 Chirality : 0.042 0.356 3033 Planarity : 0.004 0.067 3439 Dihedral : 16.220 177.283 3130 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 1.31 % Allowed : 15.18 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2342 helix: 1.84 (0.15), residues: 1127 sheet: -0.29 (0.33), residues: 270 loop : -1.42 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 632 TYR 0.022 0.001 TYR A1046 PHE 0.026 0.001 PHE B 641 TRP 0.013 0.001 TRP A 934 HIS 0.006 0.001 HIS B 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (20511) covalent geometry : angle 0.59117 / 0.30 (27876) hydrogen bonds : bond 0.04171 / 2.86 ( 939) hydrogen bonds : angle 4.35812 / 3.11 ( 2676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5391.65 seconds wall clock time: 92 minutes 57.30 seconds (5577.30 seconds total)