Starting phenix.real_space_refine on Tue Jun 17 18:14:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ix4_60964/06_2025/9ix4_60964_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ix4_60964/06_2025/9ix4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ix4_60964/06_2025/9ix4_60964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ix4_60964/06_2025/9ix4_60964.map" model { file = "/net/cci-nas-00/data/ceres_data/9ix4_60964/06_2025/9ix4_60964_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ix4_60964/06_2025/9ix4_60964_trim.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'ARG:plan': 1, 'GLN:plan1': 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: 12.96, per 1000 atoms: 0.65 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: 5.32 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 7.72 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: 9.22 Time building geometry restraints manager: 6.27 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 1.50e-02 4.44e+03 3.48e+01 bond pdb=" O3' DT C 37 " pdb=" P DC C 38 " ideal model delta sigma weight residual 1.607 1.680 -0.073 1.50e-02 4.44e+03 2.36e+01 bond pdb=" O3' DT C 35 " pdb=" P DA C 36 " ideal model delta sigma weight residual 1.607 1.537 0.070 1.50e-02 4.44e+03 2.15e+01 bond pdb=" O3' DA C 36 " pdb=" P DT C 37 " ideal model delta sigma weight residual 1.607 1.540 0.067 1.50e-02 4.44e+03 1.98e+01 bond pdb=" O3' DT D 37 " pdb=" P DC D 38 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.50e-02 4.44e+03 1.52e+01 ... (remaining 20506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 27417 2.41 - 4.83: 381 4.83 - 7.24: 59 7.24 - 9.65: 12 9.65 - 12.06: 7 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=" O3' DT C 35 " pdb=" C3' DT C 35 " pdb=" C2' DT C 35 " ideal model delta sigma weight residual 111.50 101.37 10.13 1.50e+00 4.44e-01 4.56e+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 ... (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 - 0.060: 2535 0.060 - 0.120: 435 0.120 - 0.180: 45 0.180 - 0.240: 10 0.240 - 0.300: 8 Chirality restraints: 3033 Sorted by residual: 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 chirality pdb=" C3' DA D 31 " pdb=" C4' DA D 31 " pdb=" O3' DA D 31 " pdb=" C2' DA D 31 " both_signs ideal model delta sigma weight residual False -2.66 -2.94 0.28 2.00e-01 2.50e+01 2.01e+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 1177 \ or resid 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: 4.690 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: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 55.020 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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= 0.271 Angle : 0.732 12.064 27876 Z= 0.427 Chirality : 0.048 0.300 3033 Planarity : 0.004 0.084 3439 Dihedral : 17.461 174.248 7864 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.95 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.036 0.002 TRP A1126 HIS 0.009 0.001 HIS B 829 PHE 0.024 0.002 PHE B 641 TYR 0.016 0.002 TYR B 938 ARG 0.003 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.13692 ( 939) hydrogen bonds : angle 5.93864 ( 2676) covalent geometry : bond 0.00551 (20511) covalent geometry : angle 0.73182 (27876) *********************** 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 : 2.553 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: 0.7948 (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: 0.8244 (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: 0.8690 (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) outliers start: 21 outliers final: 7 residues processed: 239 average time/residue: 1.6624 time to fit residues: 445.2579 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 : 3.571 ------------------------------------------------------------------------------- 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 200 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 216 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 342 GLN A 700 ASN A 707 GLN ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 657 GLN B 779 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.131467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.080474 restraints weight = 33809.084| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.95 r_work: 0.2890 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20511 Z= 0.134 Angle : 0.568 11.630 27876 Z= 0.301 Chirality : 0.041 0.212 3033 Planarity : 0.004 0.056 3439 Dihedral : 16.792 179.246 3141 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.30 % Rotamer: Outliers : 1.90 % Allowed : 7.20 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2342 helix: 1.63 (0.16), residues: 1120 sheet: -0.37 (0.33), residues: 251 loop : -1.67 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1126 HIS 0.006 0.001 HIS B 491 PHE 0.026 0.001 PHE B 641 TYR 0.017 0.001 TYR A1046 ARG 0.006 0.000 ARG B 828 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 939) hydrogen bonds : angle 4.57367 ( 2676) covalent geometry : bond 0.00296 (20511) covalent geometry : angle 0.56846 (27876) *********************** 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 196 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8667 (m-30) cc_final: 0.8228 (m-30) REVERT: A 638 PHE cc_start: 0.8547 (m-80) cc_final: 0.8273 (m-80) REVERT: A 671 TYR cc_start: 0.7623 (t80) cc_final: 0.6927 (t80) REVERT: A 741 MET cc_start: 0.7244 (ttm) cc_final: 0.5410 (mpt) REVERT: A 765 HIS cc_start: 0.6818 (p90) cc_final: 0.6544 (p90) REVERT: A 788 ARG cc_start: 0.8757 (mtm-85) cc_final: 0.8382 (mtm-85) REVERT: A 922 ARG cc_start: 0.7725 (tpp-160) cc_final: 0.7453 (tmm160) REVERT: A 942 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7665 (ttt180) REVERT: A 1014 MET cc_start: 0.0929 (ptt) cc_final: -0.0591 (mpt) REVERT: A 1143 MET cc_start: 0.6474 (mmm) cc_final: 0.5312 (mpt) REVERT: B 141 PHE cc_start: 0.8864 (m-80) cc_final: 0.8441 (m-80) REVERT: B 172 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8896 (tppt) REVERT: B 253 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.8795 (tppt) REVERT: B 276 GLU cc_start: 0.8402 (tp30) cc_final: 0.8169 (mm-30) REVERT: B 582 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8554 (pp) REVERT: B 586 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7419 (p90) REVERT: B 943 TRP cc_start: 0.8600 (m100) cc_final: 0.7525 (m-90) REVERT: B 977 GLU cc_start: 0.8072 (pm20) cc_final: 0.7752 (pm20) REVERT: B 979 LEU cc_start: 0.9173 (mt) cc_final: 0.8932 (mm) REVERT: B 986 LYS cc_start: 0.8378 (tttt) cc_final: 0.8078 (tmmm) REVERT: B 992 ASN cc_start: 0.8897 (t0) cc_final: 0.8517 (t160) REVERT: B 1034 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7366 (tm-30) outliers start: 39 outliers final: 11 residues processed: 183 average time/residue: 1.4117 time to fit residues: 295.1226 Evaluate side-chains 151 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1000 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 253 LYS 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 31 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 124 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 GLN 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 = 0.3872 r_free = 0.3872 target = 0.130790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079997 restraints weight = 33911.161| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.89 r_work: 0.2890 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1734 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= 0.177 Angle : 0.567 9.469 27876 Z= 0.299 Chirality : 0.041 0.239 3033 Planarity : 0.004 0.057 3439 Dihedral : 16.494 179.391 3136 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 2.04 % Allowed : 9.82 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2342 helix: 1.73 (0.16), residues: 1128 sheet: -0.45 (0.33), residues: 259 loop : -1.59 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 897 HIS 0.005 0.001 HIS B 491 PHE 0.030 0.001 PHE B 641 TYR 0.018 0.001 TYR A1046 ARG 0.007 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 939) hydrogen bonds : angle 4.43379 ( 2676) covalent geometry : bond 0.00412 (20511) covalent geometry : angle 0.56708 (27876) *********************** 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 181 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 2.364 Fit side-chains revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8436 (mm-30) REVERT: A 275 ASP cc_start: 0.8696 (m-30) cc_final: 0.8495 (m-30) REVERT: A 533 ASP cc_start: 0.8653 (m-30) cc_final: 0.8299 (m-30) REVERT: A 638 PHE cc_start: 0.8599 (m-80) cc_final: 0.8312 (m-80) REVERT: A 653 PHE cc_start: 0.7491 (t80) cc_final: 0.7267 (t80) REVERT: A 671 TYR cc_start: 0.7389 (t80) cc_final: 0.6872 (t80) REVERT: A 674 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7764 (pp20) REVERT: A 741 MET cc_start: 0.7273 (ttm) cc_final: 0.5322 (mpt) REVERT: A 765 HIS cc_start: 0.6778 (p90) cc_final: 0.6482 (p90) REVERT: A 788 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8406 (mtm-85) REVERT: A 922 ARG cc_start: 0.7858 (tpp-160) cc_final: 0.7433 (tmm160) REVERT: A 1014 MET cc_start: 0.0796 (ptt) cc_final: -0.1091 (mpt) REVERT: A 1143 MET cc_start: 0.6210 (mmm) cc_final: 0.5173 (mpt) REVERT: B 141 PHE cc_start: 0.8920 (m-80) cc_final: 0.8509 (m-80) REVERT: B 253 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8786 (tppt) REVERT: B 271 GLU cc_start: 0.8495 (tt0) cc_final: 0.7839 (tp30) REVERT: B 276 GLU cc_start: 0.8593 (tp30) cc_final: 0.8376 (mm-30) REVERT: B 313 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7519 (p90) REVERT: B 582 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8586 (pp) REVERT: B 604 TRP cc_start: 0.8471 (m100) cc_final: 0.8107 (m100) REVERT: B 726 SER cc_start: 0.9537 (t) cc_final: 0.9321 (m) REVERT: B 922 ARG cc_start: 0.8077 (mmt-90) cc_final: 0.7592 (mtp85) REVERT: B 943 TRP cc_start: 0.8738 (m100) cc_final: 0.8414 (m-90) REVERT: B 977 GLU cc_start: 0.8087 (pm20) cc_final: 0.7807 (pm20) REVERT: B 979 LEU cc_start: 0.9256 (mt) cc_final: 0.9008 (mm) REVERT: B 992 ASN cc_start: 0.8970 (t0) cc_final: 0.8532 (t160) REVERT: B 1014 MET cc_start: 0.6751 (ttm) cc_final: 0.6508 (ttm) REVERT: B 1034 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7378 (tm-30) outliers start: 42 outliers final: 13 residues processed: 166 average time/residue: 1.4819 time to fit residues: 279.2897 Evaluate side-chains 144 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 674 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 172 LYS 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 985 VAL 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 195 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.131729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.081347 restraints weight = 34131.831| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.89 r_work: 0.2910 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1994 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= 0.138 Angle : 0.536 9.269 27876 Z= 0.281 Chirality : 0.040 0.221 3033 Planarity : 0.004 0.056 3439 Dihedral : 16.403 179.647 3134 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 1.70 % Allowed : 11.53 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2342 helix: 1.83 (0.16), residues: 1129 sheet: -0.39 (0.34), residues: 259 loop : -1.51 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1126 HIS 0.006 0.001 HIS B 491 PHE 0.027 0.001 PHE B 641 TYR 0.019 0.001 TYR A1046 ARG 0.009 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 939) hydrogen bonds : angle 4.27746 ( 2676) covalent geometry : bond 0.00315 (20511) covalent geometry : angle 0.53595 (27876) *********************** 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 172 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 2.249 Fit side-chains revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8648 (m-30) cc_final: 0.8297 (m-30) REVERT: A 736 ASN cc_start: 0.8238 (m-40) cc_final: 0.8004 (m-40) REVERT: A 741 MET cc_start: 0.7278 (ttm) cc_final: 0.5257 (mpt) REVERT: A 765 HIS cc_start: 0.6805 (p90) cc_final: 0.6493 (p90) REVERT: A 788 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8412 (mtm-85) REVERT: A 852 ASN cc_start: 0.8398 (m-40) cc_final: 0.8187 (m110) REVERT: A 853 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6964 (mtt180) REVERT: A 858 MET cc_start: 0.7552 (tmt) cc_final: 0.7045 (tmm) REVERT: A 922 ARG cc_start: 0.7815 (tpp-160) cc_final: 0.7478 (tmm160) REVERT: A 1014 MET cc_start: 0.0934 (ptt) cc_final: -0.0987 (mpt) REVERT: A 1143 MET cc_start: 0.6220 (mmm) cc_final: 0.5182 (mpt) REVERT: B 141 PHE cc_start: 0.8928 (m-80) cc_final: 0.8404 (m-80) REVERT: B 253 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8769 (tppt) REVERT: B 271 GLU cc_start: 0.8523 (tt0) cc_final: 0.7872 (tp30) REVERT: B 276 GLU cc_start: 0.8548 (tp30) cc_final: 0.8320 (mm-30) REVERT: B 313 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7475 (p90) REVERT: B 582 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8611 (pp) REVERT: B 726 SER cc_start: 0.9507 (t) cc_final: 0.9248 (m) REVERT: B 922 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.7556 (mtp85) REVERT: B 943 TRP cc_start: 0.8733 (m100) cc_final: 0.8373 (m-90) REVERT: B 977 GLU cc_start: 0.8115 (pm20) cc_final: 0.7831 (pm20) REVERT: B 979 LEU cc_start: 0.9251 (mt) cc_final: 0.9003 (mm) REVERT: B 992 ASN cc_start: 0.9007 (t0) cc_final: 0.8543 (t160) outliers start: 35 outliers final: 11 residues processed: 160 average time/residue: 1.2800 time to fit residues: 235.2219 Evaluate side-chains 137 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 2.275 ------------------------------------------------------------------------------- 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 990 HIS Chi-restraints excluded: chain A residue 1000 THR 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 985 VAL 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 175 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 76 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 59 optimal weight: 0.0870 chunk 225 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN 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 = 0.3865 r_free = 0.3865 target = 0.130173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079826 restraints weight = 34205.186| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.88 r_work: 0.2883 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.004 0.043 20511 Z= 0.171 Angle : 0.545 9.739 27876 Z= 0.286 Chirality : 0.041 0.237 3033 Planarity : 0.004 0.057 3439 Dihedral : 16.346 178.271 3130 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.65 % Favored : 95.26 % Rotamer: Outliers : 1.99 % Allowed : 12.26 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.18), residues: 2342 helix: 1.85 (0.16), residues: 1129 sheet: -0.28 (0.34), residues: 258 loop : -1.48 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 934 HIS 0.006 0.001 HIS B 491 PHE 0.030 0.001 PHE B 641 TYR 0.019 0.001 TYR A1046 ARG 0.007 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 939) hydrogen bonds : angle 4.31851 ( 2676) covalent geometry : bond 0.00400 (20511) covalent geometry : angle 0.54520 (27876) *********************** 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 169 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8671 (m-30) cc_final: 0.8313 (m-30) REVERT: A 741 MET cc_start: 0.7224 (ttm) cc_final: 0.5271 (mpt) REVERT: A 765 HIS cc_start: 0.6796 (p90) cc_final: 0.6487 (p90) REVERT: A 788 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: A 852 ASN cc_start: 0.8447 (m-40) cc_final: 0.8244 (m110) REVERT: A 860 LEU cc_start: 0.6551 (tm) cc_final: 0.6316 (tm) REVERT: A 922 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7481 (tmm160) REVERT: A 1143 MET cc_start: 0.6275 (mmm) cc_final: 0.5213 (mpt) REVERT: B 140 GLU cc_start: 0.8322 (pm20) cc_final: 0.8039 (pm20) REVERT: B 141 PHE cc_start: 0.8922 (m-80) cc_final: 0.8320 (m-80) REVERT: B 276 GLU cc_start: 0.8601 (tp30) cc_final: 0.8388 (mm-30) REVERT: B 313 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7542 (p90) REVERT: B 582 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8633 (pp) REVERT: B 726 SER cc_start: 0.9494 (t) cc_final: 0.9219 (m) REVERT: B 943 TRP cc_start: 0.8742 (m100) cc_final: 0.8425 (m-90) REVERT: B 977 GLU cc_start: 0.8131 (pm20) cc_final: 0.7836 (pm20) REVERT: B 979 LEU cc_start: 0.9253 (mt) cc_final: 0.8979 (mm) REVERT: B 992 ASN cc_start: 0.9016 (t0) cc_final: 0.8532 (t160) outliers start: 41 outliers final: 16 residues processed: 161 average time/residue: 1.1901 time to fit residues: 220.6374 Evaluate side-chains 141 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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 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 173 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 12 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 218 optimal weight: 0.1980 chunk 158 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.081616 restraints weight = 34005.587| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.88 r_work: 0.2923 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20511 Z= 0.125 Angle : 0.534 9.642 27876 Z= 0.278 Chirality : 0.040 0.251 3033 Planarity : 0.004 0.060 3439 Dihedral : 16.293 178.947 3130 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 1.46 % Allowed : 13.52 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2342 helix: 1.91 (0.15), residues: 1131 sheet: -0.22 (0.34), residues: 256 loop : -1.45 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 934 HIS 0.008 0.001 HIS B 948 PHE 0.026 0.001 PHE A 565 TYR 0.026 0.001 TYR A 671 ARG 0.009 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 939) hydrogen bonds : angle 4.18715 ( 2676) covalent geometry : bond 0.00283 (20511) covalent geometry : angle 0.53384 (27876) *********************** 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 169 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 ASP cc_start: 0.8610 (m-30) cc_final: 0.8254 (m-30) REVERT: A 741 MET cc_start: 0.7036 (ttm) cc_final: 0.5158 (mpt) REVERT: A 765 HIS cc_start: 0.6709 (p90) cc_final: 0.6393 (p90) REVERT: A 788 ARG cc_start: 0.8772 (mtm-85) cc_final: 0.8445 (mtm-85) REVERT: A 852 ASN cc_start: 0.8429 (m-40) cc_final: 0.7812 (m110) REVERT: A 858 MET cc_start: 0.7520 (tmt) cc_final: 0.7070 (tmm) REVERT: A 860 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6337 (tm) REVERT: A 922 ARG cc_start: 0.7806 (tpp-160) cc_final: 0.7517 (tmm160) REVERT: A 948 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.7995 (p90) REVERT: A 1014 MET cc_start: 0.0323 (ptt) cc_final: -0.1149 (mpt) REVERT: A 1143 MET cc_start: 0.6274 (mmm) cc_final: 0.5091 (mpt) REVERT: B 139 ASN cc_start: 0.7197 (t0) cc_final: 0.6479 (t0) REVERT: B 140 GLU cc_start: 0.8321 (pm20) cc_final: 0.8055 (pm20) REVERT: B 141 PHE cc_start: 0.9003 (m-80) cc_final: 0.8406 (m-80) REVERT: B 253 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8720 (tppt) REVERT: B 276 GLU cc_start: 0.8540 (tp30) cc_final: 0.8323 (mm-30) REVERT: B 313 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7518 (p90) REVERT: B 582 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8563 (pp) REVERT: B 726 SER cc_start: 0.9502 (t) cc_final: 0.9189 (m) REVERT: B 922 ARG cc_start: 0.8077 (mmt-90) cc_final: 0.7865 (mmt-90) REVERT: B 943 TRP cc_start: 0.8750 (m100) cc_final: 0.8462 (m-90) REVERT: B 977 GLU cc_start: 0.8119 (pm20) cc_final: 0.7843 (pm20) REVERT: B 979 LEU cc_start: 0.9263 (mt) cc_final: 0.8985 (mm) REVERT: B 992 ASN cc_start: 0.9022 (t0) cc_final: 0.8520 (t160) outliers start: 30 outliers final: 16 residues processed: 159 average time/residue: 1.2953 time to fit residues: 236.4449 Evaluate side-chains 144 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 2.123 ------------------------------------------------------------------------------- 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 769 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 948 HIS 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 173 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 Chi-restraints excluded: chain B residue 1152 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 203 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 106 optimal weight: 0.0470 chunk 227 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 218 optimal weight: 0.0770 chunk 220 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN 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 = 0.3898 r_free = 0.3898 target = 0.133002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.082756 restraints weight = 33743.006| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.91 r_work: 0.2940 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 20511 Z= 0.111 Angle : 0.528 9.792 27876 Z= 0.273 Chirality : 0.040 0.296 3033 Planarity : 0.004 0.062 3439 Dihedral : 16.197 179.721 3130 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.94 % Rotamer: Outliers : 1.90 % Allowed : 13.42 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2342 helix: 1.99 (0.15), residues: 1129 sheet: -0.19 (0.34), residues: 246 loop : -1.41 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 934 HIS 0.009 0.001 HIS B 948 PHE 0.023 0.001 PHE B 641 TYR 0.021 0.001 TYR A1046 ARG 0.012 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 939) hydrogen bonds : angle 4.10887 ( 2676) covalent geometry : bond 0.00248 (20511) covalent geometry : angle 0.52756 (27876) *********************** 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 189 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 ASP cc_start: 0.8731 (m-30) cc_final: 0.8478 (m-30) REVERT: A 326 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8488 (tp40) REVERT: A 533 ASP cc_start: 0.8558 (m-30) cc_final: 0.8200 (m-30) REVERT: A 741 MET cc_start: 0.7041 (ttm) cc_final: 0.5165 (mpt) REVERT: A 765 HIS cc_start: 0.6773 (p90) cc_final: 0.6456 (p90) REVERT: A 788 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8421 (mtm-85) REVERT: A 852 ASN cc_start: 0.8428 (m-40) cc_final: 0.7921 (m110) REVERT: A 860 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6369 (tm) REVERT: A 872 MET cc_start: 0.8439 (mtp) cc_final: 0.7996 (ttp) REVERT: A 922 ARG cc_start: 0.7813 (tpp-160) cc_final: 0.7605 (tmm160) REVERT: A 948 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.7889 (p90) REVERT: A 1143 MET cc_start: 0.6243 (mmm) cc_final: 0.5050 (mpt) REVERT: B 141 PHE cc_start: 0.8977 (m-80) cc_final: 0.8622 (m-80) REVERT: B 253 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8690 (tppt) REVERT: B 276 GLU cc_start: 0.8493 (tp30) cc_final: 0.8266 (mm-30) REVERT: B 313 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7692 (p90) REVERT: B 492 ASP cc_start: 0.8859 (t70) cc_final: 0.8593 (t0) REVERT: B 582 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8563 (pp) REVERT: B 585 ARG cc_start: 0.8178 (mmm160) cc_final: 0.7949 (mmt90) REVERT: B 726 SER cc_start: 0.9526 (t) cc_final: 0.9215 (m) REVERT: B 922 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.7757 (mmt-90) REVERT: B 943 TRP cc_start: 0.8730 (m100) cc_final: 0.8405 (m-90) REVERT: B 977 GLU cc_start: 0.8113 (pm20) cc_final: 0.7818 (pm20) REVERT: B 979 LEU cc_start: 0.9266 (mt) cc_final: 0.8984 (mm) REVERT: B 992 ASN cc_start: 0.9000 (t0) cc_final: 0.8526 (t160) outliers start: 39 outliers final: 13 residues processed: 174 average time/residue: 1.2296 time to fit residues: 246.0791 Evaluate side-chains 148 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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 726 SER Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 948 HIS 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 173 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 605 GLU Chi-restraints excluded: chain B residue 948 HIS Chi-restraints excluded: chain B residue 990 HIS Chi-restraints excluded: chain B residue 1152 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 2.9990 chunk 139 optimal weight: 0.0170 chunk 79 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 99 optimal weight: 0.0020 chunk 143 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.4426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.133513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083307 restraints weight = 34017.636| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.90 r_work: 0.2964 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20511 Z= 0.111 Angle : 0.546 11.465 27876 Z= 0.279 Chirality : 0.040 0.342 3033 Planarity : 0.004 0.064 3439 Dihedral : 16.131 179.645 3130 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 1.31 % Allowed : 14.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2342 helix: 2.05 (0.15), residues: 1129 sheet: -0.15 (0.34), residues: 246 loop : -1.33 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 934 HIS 0.005 0.001 HIS B 491 PHE 0.026 0.001 PHE A 969 TYR 0.021 0.001 TYR A1046 ARG 0.012 0.000 ARG B 585 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 939) hydrogen bonds : angle 4.06409 ( 2676) covalent geometry : bond 0.00248 (20511) covalent geometry : angle 0.54608 (27876) *********************** 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 173 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ASP cc_start: 0.8737 (m-30) cc_final: 0.8463 (m-30) REVERT: A 326 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8497 (tp40) REVERT: A 533 ASP cc_start: 0.8567 (m-30) cc_final: 0.8215 (m-30) REVERT: A 577 LYS cc_start: 0.8632 (tmtt) cc_final: 0.8183 (tmtm) REVERT: A 741 MET cc_start: 0.6966 (ttm) cc_final: 0.5201 (mpt) REVERT: A 765 HIS cc_start: 0.6766 (p90) cc_final: 0.6471 (p90) REVERT: A 788 ARG cc_start: 0.8768 (mtm-85) cc_final: 0.8445 (mtm-85) REVERT: A 852 ASN cc_start: 0.8461 (m-40) cc_final: 0.8008 (m-40) REVERT: A 853 ARG cc_start: 0.7011 (mtt180) cc_final: 0.6715 (mtt180) REVERT: A 858 MET cc_start: 0.7529 (tmt) cc_final: 0.7047 (tmm) REVERT: A 860 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6169 (mp) REVERT: A 872 MET cc_start: 0.8405 (mtp) cc_final: 0.8075 (ttp) REVERT: A 948 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.7734 (p90) REVERT: A 1020 LEU cc_start: 0.5146 (OUTLIER) cc_final: 0.4253 (tm) REVERT: A 1143 MET cc_start: 0.6395 (mmm) cc_final: 0.5141 (mpt) REVERT: B 136 MET cc_start: 0.8626 (mmm) cc_final: 0.8351 (mmp) REVERT: B 139 ASN cc_start: 0.7049 (t0) cc_final: 0.6219 (t0) REVERT: B 140 GLU cc_start: 0.8249 (pm20) cc_final: 0.7856 (pm20) REVERT: B 141 PHE cc_start: 0.8964 (m-80) cc_final: 0.8516 (m-80) REVERT: B 253 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8684 (tppt) REVERT: B 276 GLU cc_start: 0.8520 (tp30) cc_final: 0.8294 (mm-30) REVERT: B 492 ASP cc_start: 0.8798 (t70) cc_final: 0.8566 (t0) REVERT: B 582 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8548 (pp) REVERT: B 726 SER cc_start: 0.9522 (t) cc_final: 0.9216 (m) REVERT: B 785 LEU cc_start: 0.8230 (tp) cc_final: 0.7799 (mp) REVERT: B 922 ARG cc_start: 0.8007 (mmt-90) cc_final: 0.7795 (mmt-90) REVERT: B 943 TRP cc_start: 0.8730 (m100) cc_final: 0.8401 (m-90) REVERT: B 977 GLU cc_start: 0.8128 (pm20) cc_final: 0.7813 (pm20) REVERT: B 979 LEU cc_start: 0.9285 (mt) cc_final: 0.9000 (mm) REVERT: B 992 ASN cc_start: 0.9005 (t0) cc_final: 0.8531 (t160) outliers start: 27 outliers final: 11 residues processed: 165 average time/residue: 1.3025 time to fit residues: 245.9103 Evaluate side-chains 150 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 2.104 ------------------------------------------------------------------------------- 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 726 SER Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 948 HIS Chi-restraints excluded: chain B residue 990 HIS Chi-restraints excluded: chain B residue 1152 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 163 optimal weight: 0.2980 chunk 182 optimal weight: 0.0770 chunk 142 optimal weight: 0.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN 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 = 0.3903 r_free = 0.3903 target = 0.133355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.083042 restraints weight = 33668.068| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.90 r_work: 0.2959 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20511 Z= 0.118 Angle : 0.556 11.741 27876 Z= 0.285 Chirality : 0.040 0.349 3033 Planarity : 0.004 0.066 3439 Dihedral : 16.139 179.719 3130 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 1.22 % Allowed : 14.69 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2342 helix: 2.07 (0.15), residues: 1129 sheet: -0.13 (0.34), residues: 245 loop : -1.30 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 934 HIS 0.015 0.001 HIS B 948 PHE 0.024 0.001 PHE B 641 TYR 0.023 0.001 TYR A1046 ARG 0.014 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 939) hydrogen bonds : angle 4.08174 ( 2676) covalent geometry : bond 0.00269 (20511) covalent geometry : angle 0.55634 (27876) *********************** 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 161 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8962 (mppt) cc_final: 0.8438 (tmmt) REVERT: A 326 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8498 (tp40) REVERT: A 533 ASP cc_start: 0.8555 (m-30) cc_final: 0.8216 (m-30) REVERT: A 577 LYS cc_start: 0.8646 (tmtt) cc_final: 0.8150 (tmtm) REVERT: A 578 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8994 (m) REVERT: A 741 MET cc_start: 0.6875 (ttm) cc_final: 0.5111 (mpt) REVERT: A 788 ARG cc_start: 0.8824 (mtm-85) cc_final: 0.8522 (mtm-85) REVERT: A 852 ASN cc_start: 0.8448 (m-40) cc_final: 0.7907 (m-40) REVERT: A 860 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6183 (mp) REVERT: A 872 MET cc_start: 0.8379 (mtp) cc_final: 0.8054 (ttp) REVERT: A 948 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.7708 (p90) REVERT: A 1020 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4325 (tm) REVERT: A 1143 MET cc_start: 0.6382 (mmm) cc_final: 0.5203 (mpt) REVERT: B 141 PHE cc_start: 0.9053 (m-80) cc_final: 0.8696 (m-80) REVERT: B 276 GLU cc_start: 0.8523 (tp30) cc_final: 0.8311 (mm-30) REVERT: B 492 ASP cc_start: 0.8828 (t70) cc_final: 0.8604 (t0) REVERT: B 582 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8586 (pp) REVERT: B 726 SER cc_start: 0.9524 (t) cc_final: 0.9220 (m) REVERT: B 785 LEU cc_start: 0.8247 (tp) cc_final: 0.7818 (mp) REVERT: B 922 ARG cc_start: 0.7951 (mmt-90) cc_final: 0.7708 (mmp80) REVERT: B 943 TRP cc_start: 0.8729 (m100) cc_final: 0.8381 (m-90) REVERT: B 977 GLU cc_start: 0.8130 (pm20) cc_final: 0.7863 (pm20) REVERT: B 979 LEU cc_start: 0.9291 (mt) cc_final: 0.9005 (mm) REVERT: B 992 ASN cc_start: 0.9005 (t0) cc_final: 0.8535 (t160) outliers start: 25 outliers final: 13 residues processed: 153 average time/residue: 1.2446 time to fit residues: 219.4015 Evaluate side-chains 148 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 276 GLU 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 860 LEU Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 948 HIS 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 49 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 HIS ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN B 948 HIS ** 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 = 0.3847 r_free = 0.3847 target = 0.129198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078526 restraints weight = 33949.583| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.89 r_work: 0.2871 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20511 Z= 0.218 Angle : 0.623 11.080 27876 Z= 0.320 Chirality : 0.043 0.345 3033 Planarity : 0.004 0.067 3439 Dihedral : 16.231 176.362 3130 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 1.22 % Allowed : 14.93 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2342 helix: 1.92 (0.16), residues: 1131 sheet: -0.34 (0.34), residues: 251 loop : -1.38 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 934 HIS 0.022 0.001 HIS B 948 PHE 0.032 0.002 PHE B 641 TYR 0.045 0.002 TYR B 938 ARG 0.019 0.001 ARG B 585 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 939) hydrogen bonds : angle 4.35077 ( 2676) covalent geometry : bond 0.00511 (20511) covalent geometry : angle 0.62261 (27876) ********************** 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 159 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.8639 (t0) cc_final: 0.8175 (t0) REVERT: A 172 LYS cc_start: 0.8968 (mppt) cc_final: 0.8397 (tmmt) REVERT: A 275 ASP cc_start: 0.8730 (m-30) cc_final: 0.8519 (m-30) REVERT: A 533 ASP cc_start: 0.8674 (m-30) cc_final: 0.8314 (m-30) REVERT: A 741 MET cc_start: 0.7008 (ttm) cc_final: 0.5189 (mpt) REVERT: A 765 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.6273 (p90) REVERT: A 788 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8524 (mtm-85) REVERT: A 852 ASN cc_start: 0.8583 (m-40) cc_final: 0.8060 (m110) REVERT: A 858 MET cc_start: 0.7546 (tmt) cc_final: 0.6962 (tmm) REVERT: A 860 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6803 (tm) REVERT: A 1020 LEU cc_start: 0.5251 (OUTLIER) cc_final: 0.4355 (tm) REVERT: A 1143 MET cc_start: 0.6252 (mmm) cc_final: 0.5076 (mpt) REVERT: B 139 ASN cc_start: 0.6957 (t0) cc_final: 0.6689 (t0) REVERT: B 141 PHE cc_start: 0.8983 (m-80) cc_final: 0.8651 (m-80) REVERT: B 276 GLU cc_start: 0.8678 (tp30) cc_final: 0.8428 (mm-30) REVERT: B 582 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8617 (pp) REVERT: B 585 ARG cc_start: 0.8352 (mmm160) cc_final: 0.8092 (mmt90) REVERT: B 726 SER cc_start: 0.9522 (t) cc_final: 0.9177 (m) REVERT: B 851 MET cc_start: 0.9250 (ptm) cc_final: 0.8933 (ptp) REVERT: B 943 TRP cc_start: 0.8794 (m100) cc_final: 0.8431 (m-90) REVERT: B 977 GLU cc_start: 0.8168 (pm20) cc_final: 0.7874 (pm20) REVERT: B 979 LEU cc_start: 0.9268 (mt) cc_final: 0.8973 (mm) REVERT: B 992 ASN cc_start: 0.9012 (t0) cc_final: 0.8532 (t160) outliers start: 25 outliers final: 15 residues processed: 155 average time/residue: 1.1906 time to fit residues: 214.0706 Evaluate side-chains 148 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 276 GLU 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 860 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 236 THR 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 948 HIS 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 9 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 HIS ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN 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 = 0.3871 r_free = 0.3871 target = 0.130968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.080432 restraints weight = 33871.756| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.89 r_work: 0.2894 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20511 Z= 0.145 Angle : 0.586 11.787 27876 Z= 0.299 Chirality : 0.041 0.352 3033 Planarity : 0.004 0.078 3439 Dihedral : 16.129 177.067 3130 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 1.12 % Allowed : 14.83 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2342 helix: 1.97 (0.15), residues: 1131 sheet: -0.31 (0.33), residues: 255 loop : -1.29 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 943 HIS 0.010 0.001 HIS B 948 PHE 0.026 0.001 PHE B 641 TYR 0.044 0.001 TYR B 938 ARG 0.019 0.001 ARG B 585 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 939) hydrogen bonds : angle 4.23732 ( 2676) covalent geometry : bond 0.00335 (20511) covalent geometry : angle 0.58593 (27876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11877.53 seconds wall clock time: 205 minutes 53.00 seconds (12353.00 seconds total)