Starting phenix.real_space_refine on Fri Aug 7 10:11:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ixm_60973/08_2026/9ixm_60973.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ixm_60973/08_2026/9ixm_60973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ixm_60973/08_2026/9ixm_60973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ixm_60973/08_2026/9ixm_60973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ixm_60973/08_2026/9ixm_60973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ixm_60973/08_2026/9ixm_60973.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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: 6 Type Number sf(0) Gaussians P 75 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 13107 2.51 5 N 3651 2.21 5 O 4028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20925 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9459 Classifications: {'peptide': 1169} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1130} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 5848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5848 Classifications: {'peptide': 713} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 682} Chain: "C" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4076 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 15, 'TRANS': 505} Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 3, 'HIS:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 622 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.81, per 1000 atoms: 0.23 Number of scatterers: 20925 At special positions: 0 Unit cell: (129.548, 124.888, 147.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 75 15.00 Mg 1 11.99 O 4028 8.00 N 3651 7.00 C 13107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 888.8 milliseconds 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 20 sheets defined 50.1% alpha, 11.6% beta 10 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.669A pdb=" N PHE A 6 " --> pdb=" O GLN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 31 removed outlier: 3.635A pdb=" N THR A 31 " --> pdb=" O PRO A 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 31' Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 116 through 138 removed outlier: 3.677A pdb=" N MET A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 169 Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.534A pdb=" N ASP A 217 " --> pdb=" O PRO A 214 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 218' Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 247 through 253 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 264 through 280 removed outlier: 4.221A pdb=" N GLN A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 299 removed outlier: 3.667A pdb=" N ASN A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 313 Processing helix chain 'A' and resid 314 through 332 removed outlier: 4.047A pdb=" N LYS A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 420 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 443 through 455 removed outlier: 3.934A pdb=" N LEU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 505 through 515 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.545A pdb=" N LEU A 555 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.525A pdb=" N ILE A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 599 through 616 removed outlier: 3.634A pdb=" N ILE A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 646 removed outlier: 4.398A pdb=" N PHE A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 684 Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 761 through 764 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: 3.513A 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 873 Processing helix chain 'A' and resid 884 through 894 Processing helix chain 'A' and resid 901 through 927 Processing helix chain 'A' and resid 931 through 948 removed outlier: 3.804A pdb=" N ALA A 935 " --> pdb=" O SER A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 958 Processing helix chain 'A' and resid 959 through 966 removed outlier: 3.743A pdb=" N ASP A 966 " --> pdb=" O PHE A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1016 Processing helix chain 'A' and resid 1019 through 1027 Processing helix chain 'A' and resid 1041 through 1065 removed outlier: 3.783A pdb=" N ASN A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1079 Processing helix chain 'A' and resid 1103 through 1123 removed outlier: 3.832A pdb=" N GLU A1107 " --> pdb=" O ASP A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1177 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 37 through 48 Processing helix chain 'B' and resid 87 through 95 removed outlier: 4.632A pdb=" N GLY B 92 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE B 94 " --> pdb=" O MET B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 223 through 239 Processing helix chain 'B' and resid 264 through 271 removed outlier: 3.882A pdb=" N ILE B 268 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRP B 269 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 270 " --> pdb=" O THR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 302 removed outlier: 3.509A pdb=" N LEU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 308 Processing helix chain 'B' and resid 378 through 381 removed outlier: 3.768A pdb=" N ARG B 381 " --> pdb=" O ASP B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 382 through 401 Processing helix chain 'B' and resid 408 through 415 removed outlier: 3.942A pdb=" N SER B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 413 " --> pdb=" O LYS B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 475 Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 510 through 521 Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 546 through 561 removed outlier: 4.209A pdb=" N THR B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 579 Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.643A pdb=" N GLN B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 681 removed outlier: 4.169A pdb=" N ASP B 670 " --> pdb=" O ALA B 666 " (cutoff:3.500A) Proline residue: B 674 - end of helix Processing helix chain 'B' and resid 695 through 709 removed outlier: 3.551A pdb=" N TYR B 699 " --> pdb=" O TYR B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 removed outlier: 3.844A pdb=" N LYS C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU C 13 " --> pdb=" O MET C 9 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.553A pdb=" N ILE C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 76 removed outlier: 3.548A pdb=" N GLU C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 71 " --> pdb=" O ASP C 67 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 116 through 139 removed outlier: 3.505A pdb=" N LYS C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 169 removed outlier: 4.596A pdb=" N ALA C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 201 removed outlier: 3.520A pdb=" N LYS C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 214 through 218 removed outlier: 3.830A pdb=" N ASP C 217 " --> pdb=" O PRO C 214 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU C 218 " --> pdb=" O THR C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 214 through 218' Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.538A pdb=" N TYR C 248 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Proline residue: C 250 - end of helix Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 266 through 280 Processing helix chain 'C' and resid 284 through 300 removed outlier: 3.538A pdb=" N ASN C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 313 removed outlier: 3.711A pdb=" N PHE C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 removed outlier: 3.897A pdb=" N GLU C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 420 Proline residue: C 392 - end of helix Processing helix chain 'C' and resid 430 through 440 Processing helix chain 'C' and resid 443 through 455 Processing helix chain 'C' and resid 505 through 517 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 791 through 806 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 removed outlier: 6.369A pdb=" N PHE A 54 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP A 260 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 56 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 53 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU A 226 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE A 55 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 88 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N THR A 227 " --> pdb=" O ALA A 88 " (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 removed outlier: 7.291A pdb=" N GLN A 494 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASP A 488 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 365 Processing sheet with id=AA5, first strand: chain 'A' and resid 575 through 581 removed outlier: 6.677A pdb=" N SER A 652 " --> pdb=" O GLY A 771 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR A 773 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 654 " --> pdb=" O TYR A 773 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 653 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 739 through 740 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 950 through 951 Processing sheet with id=AA9, first strand: chain 'A' and resid 994 through 996 removed outlier: 3.735A pdb=" N GLN A 994 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 983 " --> pdb=" O VAL A1004 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1070 through 1071 removed outlier: 6.836A pdb=" N VAL A1128 " --> pdb=" O LEU A1150 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE A1152 " --> pdb=" O VAL A1128 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE A1130 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 253 removed outlier: 5.453A pdb=" N LYS B 15 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG B 11 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER B 252 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR B 9 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG B 8 " --> pdb=" O MET B 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 52 through 54 removed outlier: 3.518A pdb=" N ALA B 52 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE B 27 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 29 " --> pdb=" O HIS B 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.510A pdb=" N ARG B 134 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 196 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE B 175 " --> pdb=" O CYS B 188 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU B 126 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 125 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 212 through 213 removed outlier: 3.556A pdb=" N LEU B 212 " --> pdb=" O VAL B 650 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 311 through 314 removed outlier: 5.929A pdb=" N LEU B 277 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 322 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 324 " --> pdb=" O ASN B 278 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY B 321 " --> pdb=" O ILE B 347 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLN B 349 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN B 323 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 351 " --> pdb=" O ASN B 323 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 325 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 451 through 454 removed outlier: 4.820A pdb=" N GLU B 432 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE B 422 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASP B 488 " --> pdb=" O PHE B 422 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS B 489 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN B 497 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 636 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 623 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 526 through 528 Processing sheet with id=AB9, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AC1, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AC2, first strand: chain 'C' and resid 282 through 283 removed outlier: 4.048A pdb=" N ALA C 282 " --> pdb=" O ALA C 499 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2658 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3460 1.32 - 1.45: 5995 1.45 - 1.57: 11780 1.57 - 1.69: 148 1.69 - 1.82: 112 Bond restraints: 21495 Sorted by residual: bond pdb=" C1' DT F 30 " pdb=" N1 DT F 30 " ideal model delta sigma weight residual 1.468 1.565 -0.097 1.40e-02 5.10e+03 4.78e+01 bond pdb=" C1' DT F 17 " pdb=" N1 DT F 17 " ideal model delta sigma weight residual 1.468 1.560 -0.092 1.40e-02 5.10e+03 4.32e+01 bond pdb=" C1' DC F 16 " pdb=" N1 DC F 16 " ideal model delta sigma weight residual 1.468 1.553 -0.085 1.40e-02 5.10e+03 3.72e+01 bond pdb=" C1' DT F 7 " pdb=" N1 DT F 7 " ideal model delta sigma weight residual 1.468 1.553 -0.085 1.40e-02 5.10e+03 3.69e+01 bond pdb=" C1' DC E 24 " pdb=" N1 DC E 24 " ideal model delta sigma weight residual 1.468 1.551 -0.083 1.40e-02 5.10e+03 3.52e+01 ... (remaining 21490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.05: 29214 6.05 - 12.11: 84 12.11 - 18.16: 10 18.16 - 24.22: 2 24.22 - 30.27: 2 Bond angle restraints: 29312 Sorted by residual: angle pdb=" C MET A 427 " pdb=" CA MET A 427 " pdb=" CB MET A 427 " ideal model delta sigma weight residual 110.06 79.79 30.27 1.39e+00 5.18e-01 4.74e+02 angle pdb=" N GLU A 430 " pdb=" CA GLU A 430 " pdb=" C GLU A 430 " ideal model delta sigma weight residual 113.43 92.60 20.83 1.26e+00 6.30e-01 2.73e+02 angle pdb=" N VAL C 376 " pdb=" CA VAL C 376 " pdb=" C VAL C 376 " ideal model delta sigma weight residual 110.82 126.71 -15.89 9.70e-01 1.06e+00 2.68e+02 angle pdb=" N GLU C 430 " pdb=" CA GLU C 430 " pdb=" C GLU C 430 " ideal model delta sigma weight residual 113.55 94.88 18.67 1.26e+00 6.30e-01 2.20e+02 angle pdb=" N ASN A 139 " pdb=" CA ASN A 139 " pdb=" C ASN A 139 " ideal model delta sigma weight residual 110.80 139.44 -28.64 2.13e+00 2.20e-01 1.81e+02 ... (remaining 29307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 11991 33.80 - 67.60: 831 67.60 - 101.40: 41 101.40 - 135.19: 2 135.19 - 168.99: 2 Dihedral angle restraints: 12867 sinusoidal: 5803 harmonic: 7064 Sorted by residual: dihedral pdb=" C MET A 427 " pdb=" N MET A 427 " pdb=" CA MET A 427 " pdb=" CB MET A 427 " ideal model delta harmonic sigma weight residual -122.60 -85.86 -36.74 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" N LEU C 377 " pdb=" C LEU C 377 " pdb=" CA LEU C 377 " pdb=" CB LEU C 377 " ideal model delta harmonic sigma weight residual 122.80 138.70 -15.90 0 2.50e+00 1.60e-01 4.05e+01 dihedral pdb=" C PRO C 28 " pdb=" N PRO C 28 " pdb=" CA PRO C 28 " pdb=" CB PRO C 28 " ideal model delta harmonic sigma weight residual -120.70 -104.83 -15.87 0 2.50e+00 1.60e-01 4.03e+01 ... (remaining 12864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 3170 0.155 - 0.309: 31 0.309 - 0.464: 8 0.464 - 0.618: 4 0.618 - 0.773: 2 Chirality restraints: 3215 Sorted by residual: chirality pdb=" CA ASN A 139 " pdb=" N ASN A 139 " pdb=" C ASN A 139 " pdb=" CB ASN A 139 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" CA LEU C 377 " pdb=" N LEU C 377 " pdb=" C LEU C 377 " pdb=" CB LEU C 377 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CA MET A 427 " pdb=" N MET A 427 " pdb=" C MET A 427 " pdb=" CB MET A 427 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.53 2.00e-01 2.50e+01 7.05e+00 ... (remaining 3212 not shown) Planarity restraints: 3517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 213 " 0.077 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO A 214 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 407 " -0.073 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO B 408 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 408 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 408 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 47 " -0.047 2.00e-02 2.50e+03 1.76e-02 9.30e+00 pdb=" N9 DG E 47 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DG E 47 " 0.016 2.00e-02 2.50e+03 pdb=" N7 DG E 47 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG E 47 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG E 47 " -0.008 2.00e-02 2.50e+03 pdb=" O6 DG E 47 " -0.018 2.00e-02 2.50e+03 pdb=" N1 DG E 47 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DG E 47 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG E 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG E 47 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DG E 47 " 0.013 2.00e-02 2.50e+03 ... (remaining 3514 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 42 2.30 - 2.95: 9818 2.95 - 3.60: 32101 3.60 - 4.25: 49174 4.25 - 4.90: 80720 Nonbonded interactions: 171855 Sorted by model distance: nonbonded pdb=" NH1 ARG C 473 " pdb=" O ASP C 805 " model vdw 1.655 3.120 nonbonded pdb=" SD MET A 136 " pdb=" OE2 GLU A 140 " model vdw 1.660 3.400 nonbonded pdb=" N2 DG F 34 " pdb=" O2 DT F 35 " model vdw 1.867 3.120 nonbonded pdb=" CD1 LEU C 480 " pdb=" CG2 ILE C 797 " model vdw 2.116 3.880 nonbonded pdb=" O GLN A 622 " pdb=" NE2 GLN A 622 " model vdw 2.145 3.120 ... (remaining 171850 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.004 0.097 21495 Z= 0.297 Angle : 0.945 30.274 29312 Z= 0.608 Chirality : 0.057 0.773 3215 Planarity : 0.005 0.116 3517 Dihedral : 20.100 168.992 8277 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.63 % Favored : 94.70 % Rotamer: Outliers : 1.97 % Allowed : 22.39 % Favored : 75.64 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2377 helix: 1.16 (0.16), residues: 1115 sheet: -1.52 (0.28), residues: 335 loop : -1.65 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 106 TYR 0.024 0.001 TYR A 945 PHE 0.020 0.001 PHE B 634 TRP 0.015 0.001 TRP C 104 HIS 0.006 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.30 (21495) covalent geometry : angle 0.94461 / 0.61 (29312) hydrogen bonds : bond 0.16600 / 10.92 ( 949) hydrogen bonds : angle 6.87781 / 4.89 ( 2708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 LYS cc_start: 0.9096 (ttmt) cc_final: 0.8736 (tppt) REVERT: A 385 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7965 (pp) REVERT: A 787 PHE cc_start: 0.8517 (t80) cc_final: 0.8270 (t80) REVERT: A 851 MET cc_start: 0.8851 (mtp) cc_final: 0.8437 (mtp) REVERT: B 588 MET cc_start: 0.8793 (tpt) cc_final: 0.8551 (tpt) REVERT: C 261 GLU cc_start: 0.8287 (tp30) cc_final: 0.8066 (mm-30) REVERT: C 790 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8901 (t0) REVERT: C 802 TYR cc_start: 0.5747 (OUTLIER) cc_final: 0.5380 (t80) outliers start: 41 outliers final: 18 residues processed: 135 average time/residue: 0.1715 time to fit residues: 35.8527 Evaluate side-chains 114 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 802 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 972 GLN ** A1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN C 374 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.082445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059642 restraints weight = 62615.132| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.96 r_work: 0.2836 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21495 Z= 0.175 Angle : 0.653 10.936 29312 Z= 0.351 Chirality : 0.043 0.239 3215 Planarity : 0.005 0.075 3517 Dihedral : 18.572 169.083 3508 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.46 % Favored : 95.29 % Rotamer: Outliers : 2.55 % Allowed : 20.90 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2377 helix: 1.47 (0.16), residues: 1114 sheet: -1.36 (0.29), residues: 325 loop : -1.48 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 114 TYR 0.018 0.001 TYR A 945 PHE 0.012 0.001 PHE C 387 TRP 0.014 0.001 TRP A 147 HIS 0.004 0.001 HIS C 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (21495) covalent geometry : angle 0.65294 / 0.35 (29312) hydrogen bonds : bond 0.05045 / 3.31 ( 949) hydrogen bonds : angle 5.15549 / 3.65 ( 2708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 103 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 385 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7748 (pp) REVERT: A 427 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7830 (mmm) REVERT: A 622 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: A 1089 VAL cc_start: 0.6903 (OUTLIER) cc_final: 0.6517 (t) REVERT: C 149 MET cc_start: 0.8994 (ttp) cc_final: 0.8678 (ptm) REVERT: C 275 ASP cc_start: 0.8313 (m-30) cc_final: 0.8102 (m-30) REVERT: C 278 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7918 (mm) REVERT: C 365 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.6881 (m110) REVERT: C 790 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7659 (t0) outliers start: 53 outliers final: 11 residues processed: 150 average time/residue: 0.1485 time to fit residues: 35.3358 Evaluate side-chains 112 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 953 ASP Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 794 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 166 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 239 optimal weight: 40.0000 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 302 GLN ** A1084 HIS ** 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 = 0.3564 r_free = 0.3564 target = 0.082084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059294 restraints weight = 62026.473| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.83 r_work: 0.2832 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21495 Z= 0.155 Angle : 0.598 10.626 29312 Z= 0.323 Chirality : 0.042 0.309 3215 Planarity : 0.004 0.062 3517 Dihedral : 18.540 172.538 3477 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.21 % Favored : 95.58 % Rotamer: Outliers : 2.50 % Allowed : 20.75 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2377 helix: 1.59 (0.15), residues: 1122 sheet: -1.21 (0.29), residues: 316 loop : -1.40 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 351 TYR 0.018 0.001 TYR B 690 PHE 0.025 0.001 PHE C 141 TRP 0.009 0.001 TRP A 147 HIS 0.008 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (21495) covalent geometry : angle 0.59808 / 0.32 (29312) hydrogen bonds : bond 0.04265 / 2.80 ( 949) hydrogen bonds : angle 4.77930 / 3.38 ( 2708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 101 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7723 (pp) REVERT: A 622 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8048 (tp-100) REVERT: A 633 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7585 (ptm160) REVERT: A 851 MET cc_start: 0.8764 (ttm) cc_final: 0.8480 (mtp) REVERT: A 1014 MET cc_start: 0.7873 (mmt) cc_final: 0.7598 (mmm) REVERT: A 1025 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8630 (mt-10) REVERT: A 1091 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.6966 (tp) REVERT: B 680 MET cc_start: 0.8990 (mtt) cc_final: 0.8788 (mtm) REVERT: C 149 MET cc_start: 0.9027 (ttp) cc_final: 0.8724 (ptm) REVERT: C 275 ASP cc_start: 0.8345 (m-30) cc_final: 0.8066 (m-30) REVERT: C 365 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7269 (m-40) REVERT: C 790 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7597 (t0) REVERT: C 803 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8156 (mm) outliers start: 52 outliers final: 24 residues processed: 147 average time/residue: 0.1541 time to fit residues: 36.1147 Evaluate side-chains 120 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 803 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 187 optimal weight: 0.0770 chunk 204 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 GLN A1158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.081934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.057717 restraints weight = 62323.393| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.79 r_work: 0.2827 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21495 Z= 0.172 Angle : 0.584 9.823 29312 Z= 0.313 Chirality : 0.042 0.347 3215 Planarity : 0.004 0.050 3517 Dihedral : 18.500 174.149 3471 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.42 % Favored : 95.37 % Rotamer: Outliers : 2.74 % Allowed : 20.80 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2377 helix: 1.68 (0.16), residues: 1121 sheet: -1.14 (0.29), residues: 316 loop : -1.34 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.019 0.001 TYR B 690 PHE 0.018 0.001 PHE C 141 TRP 0.010 0.001 TRP A 147 HIS 0.005 0.001 HIS C 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (21495) covalent geometry : angle 0.58418 / 0.31 (29312) hydrogen bonds : bond 0.04039 / 2.65 ( 949) hydrogen bonds : angle 4.62662 / 3.26 ( 2708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 93 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7999 (mmtm) REVERT: A 385 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7802 (pp) REVERT: A 622 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8015 (tp-100) REVERT: A 633 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7635 (ptm160) REVERT: A 650 MET cc_start: 0.8615 (mmm) cc_final: 0.8387 (mmp) REVERT: A 720 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8759 (ptpt) REVERT: A 784 ASN cc_start: 0.8706 (t0) cc_final: 0.8404 (p0) REVERT: A 954 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8710 (tptp) REVERT: A 1025 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8631 (mt-10) REVERT: A 1089 VAL cc_start: 0.6937 (OUTLIER) cc_final: 0.6615 (t) REVERT: A 1091 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7004 (tp) REVERT: B 67 MET cc_start: 0.9175 (mmm) cc_final: 0.8851 (mmm) REVERT: B 106 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9294 (mt) REVERT: C 149 MET cc_start: 0.9041 (ttp) cc_final: 0.8751 (ptm) REVERT: C 274 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7628 (tp) REVERT: C 275 ASP cc_start: 0.8358 (m-30) cc_final: 0.8048 (m-30) REVERT: C 278 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7830 (mm) REVERT: C 326 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8680 (tm-30) REVERT: C 790 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7661 (t0) REVERT: C 803 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8148 (mm) outliers start: 57 outliers final: 25 residues processed: 145 average time/residue: 0.1515 time to fit residues: 34.8483 Evaluate side-chains 131 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 720 LYS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 803 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 11 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 33 optimal weight: 0.0670 chunk 167 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN B 270 GLN B 308 ASN B 633 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.057926 restraints weight = 62162.359| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.80 r_work: 0.2832 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21495 Z= 0.144 Angle : 0.561 9.607 29312 Z= 0.299 Chirality : 0.041 0.313 3215 Planarity : 0.004 0.045 3517 Dihedral : 18.532 176.346 3471 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.12 % Favored : 95.67 % Rotamer: Outliers : 2.55 % Allowed : 20.70 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.18), residues: 2377 helix: 1.70 (0.15), residues: 1128 sheet: -1.10 (0.28), residues: 324 loop : -1.25 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1108 TYR 0.018 0.001 TYR B 690 PHE 0.014 0.001 PHE C 141 TRP 0.009 0.001 TRP A 147 HIS 0.006 0.001 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21495) covalent geometry : angle 0.56071 / 0.30 (29312) hydrogen bonds : bond 0.03791 / 2.48 ( 949) hydrogen bonds : angle 4.48795 / 3.16 ( 2708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 92 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8739 (ttm) cc_final: 0.8468 (ttm) REVERT: A 137 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7976 (mmtm) REVERT: A 240 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: A 309 LYS cc_start: 0.9245 (ttmt) cc_final: 0.8945 (tppt) REVERT: A 385 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7874 (pp) REVERT: A 622 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8136 (tp-100) REVERT: A 633 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7627 (ptm160) REVERT: A 784 ASN cc_start: 0.8705 (t0) cc_final: 0.8416 (p0) REVERT: A 954 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8721 (tptp) REVERT: A 1014 MET cc_start: 0.7628 (mtt) cc_final: 0.7384 (mmm) REVERT: A 1089 VAL cc_start: 0.6985 (OUTLIER) cc_final: 0.6683 (t) REVERT: A 1091 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7050 (tp) REVERT: B 67 MET cc_start: 0.9120 (mmm) cc_final: 0.8871 (mmm) REVERT: B 106 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9279 (mt) REVERT: B 173 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8210 (mtmm) REVERT: B 680 MET cc_start: 0.9075 (mtm) cc_final: 0.8548 (mtm) REVERT: C 149 MET cc_start: 0.9035 (ttp) cc_final: 0.8741 (ptm) REVERT: C 274 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7600 (tp) REVERT: C 275 ASP cc_start: 0.8389 (m-30) cc_final: 0.8062 (m-30) REVERT: C 278 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7832 (mm) REVERT: C 326 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8685 (tm-30) REVERT: C 350 MET cc_start: 0.6869 (mpp) cc_final: 0.6658 (mpp) REVERT: C 803 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8174 (mm) outliers start: 53 outliers final: 23 residues processed: 140 average time/residue: 0.1641 time to fit residues: 35.6965 Evaluate side-chains 128 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 803 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 224 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 149 optimal weight: 0.0370 chunk 182 optimal weight: 2.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 GLN B 355 ASN B 633 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.080454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057066 restraints weight = 61837.694| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.81 r_work: 0.2774 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21495 Z= 0.232 Angle : 0.606 9.293 29312 Z= 0.322 Chirality : 0.043 0.307 3215 Planarity : 0.004 0.043 3517 Dihedral : 18.587 177.479 3467 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.80 % Favored : 94.95 % Rotamer: Outliers : 2.65 % Allowed : 20.32 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2377 helix: 1.67 (0.15), residues: 1126 sheet: -1.15 (0.29), residues: 326 loop : -1.31 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1108 TYR 0.026 0.002 TYR B 690 PHE 0.019 0.002 PHE B 673 TRP 0.010 0.001 TRP A 357 HIS 0.007 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (21495) covalent geometry : angle 0.60558 / 0.32 (29312) hydrogen bonds : bond 0.04206 / 2.76 ( 949) hydrogen bonds : angle 4.53823 / 3.19 ( 2708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 90 time to evaluate : 0.915 Fit side-chains REVERT: A 108 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: A 240 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: A 385 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7845 (pp) REVERT: A 954 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8727 (tptp) REVERT: A 1072 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6030 (t80) REVERT: A 1089 VAL cc_start: 0.7091 (OUTLIER) cc_final: 0.6845 (t) REVERT: A 1091 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7040 (tp) REVERT: B 173 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8382 (mtmm) REVERT: B 360 GLN cc_start: 0.8665 (mp10) cc_final: 0.8415 (mp10) REVERT: B 680 MET cc_start: 0.9136 (mtm) cc_final: 0.8651 (mtm) REVERT: C 149 MET cc_start: 0.9044 (ttp) cc_final: 0.8729 (ptm) REVERT: C 274 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7587 (tp) REVERT: C 275 ASP cc_start: 0.8390 (m-30) cc_final: 0.8096 (m-30) REVERT: C 278 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7885 (mm) REVERT: C 385 LEU cc_start: 0.4984 (OUTLIER) cc_final: 0.4461 (pp) REVERT: C 389 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8298 (ttp-110) REVERT: C 803 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8182 (mm) outliers start: 55 outliers final: 24 residues processed: 140 average time/residue: 0.1612 time to fit residues: 35.5885 Evaluate side-chains 124 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 1072 PHE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 803 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 238 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 219 optimal weight: 0.0470 chunk 26 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.081809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.058576 restraints weight = 62046.155| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.95 r_work: 0.2797 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21495 Z= 0.131 Angle : 0.548 11.304 29312 Z= 0.293 Chirality : 0.041 0.310 3215 Planarity : 0.004 0.044 3517 Dihedral : 18.462 179.210 3460 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.91 % Favored : 95.84 % Rotamer: Outliers : 2.26 % Allowed : 20.46 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2377 helix: 1.74 (0.15), residues: 1125 sheet: -1.12 (0.29), residues: 318 loop : -1.24 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 373 TYR 0.017 0.001 TYR B 690 PHE 0.014 0.001 PHE C 397 TRP 0.011 0.001 TRP A 147 HIS 0.005 0.001 HIS C 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21495) covalent geometry : angle 0.54820 / 0.29 (29312) hydrogen bonds : bond 0.03708 / 2.43 ( 949) hydrogen bonds : angle 4.40981 / 3.10 ( 2708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: A 240 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: A 309 LYS cc_start: 0.9237 (ttmt) cc_final: 0.8926 (tppt) REVERT: A 385 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8040 (pp) REVERT: A 784 ASN cc_start: 0.8717 (t0) cc_final: 0.8417 (p0) REVERT: A 954 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8740 (tptp) REVERT: A 1014 MET cc_start: 0.7572 (mtt) cc_final: 0.7370 (mmm) REVERT: A 1072 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6036 (t80) REVERT: A 1089 VAL cc_start: 0.6986 (OUTLIER) cc_final: 0.6717 (t) REVERT: A 1091 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7032 (tp) REVERT: A 1131 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.7107 (mp) REVERT: B 8 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8909 (ptp90) REVERT: B 173 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8370 (mtmm) REVERT: B 360 GLN cc_start: 0.8718 (mp10) cc_final: 0.8459 (mp10) REVERT: B 680 MET cc_start: 0.9147 (mtm) cc_final: 0.8730 (mtm) REVERT: C 149 MET cc_start: 0.9061 (ttp) cc_final: 0.8752 (ptm) REVERT: C 274 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7503 (tp) REVERT: C 275 ASP cc_start: 0.8386 (m-30) cc_final: 0.8086 (m-30) REVERT: C 278 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7813 (mm) REVERT: C 326 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8669 (tm-30) REVERT: C 350 MET cc_start: 0.6781 (mpp) cc_final: 0.6568 (mpp) REVERT: C 427 MET cc_start: 0.8429 (mmm) cc_final: 0.8170 (mmt) REVERT: C 803 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8187 (mm) outliers start: 47 outliers final: 27 residues processed: 136 average time/residue: 0.1597 time to fit residues: 34.8644 Evaluate side-chains 133 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 965 ARG Chi-restraints excluded: chain A residue 1072 PHE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 803 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 97 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 161 optimal weight: 0.0670 chunk 86 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 31 optimal weight: 4.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.082052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.057969 restraints weight = 61224.150| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.76 r_work: 0.2831 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21495 Z= 0.125 Angle : 0.537 9.767 29312 Z= 0.287 Chirality : 0.040 0.295 3215 Planarity : 0.004 0.043 3517 Dihedral : 18.397 179.231 3460 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.00 % Favored : 95.75 % Rotamer: Outliers : 2.31 % Allowed : 20.22 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2377 helix: 1.80 (0.15), residues: 1126 sheet: -1.09 (0.29), residues: 318 loop : -1.17 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 140 TYR 0.017 0.001 TYR B 690 PHE 0.015 0.001 PHE C 397 TRP 0.009 0.001 TRP A 147 HIS 0.005 0.001 HIS C 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (21495) covalent geometry : angle 0.53659 / 0.29 (29312) hydrogen bonds : bond 0.03595 / 2.36 ( 949) hydrogen bonds : angle 4.32010 / 3.05 ( 2708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: A 240 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: A 309 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8933 (tppt) REVERT: A 385 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8046 (pp) REVERT: A 784 ASN cc_start: 0.8676 (t0) cc_final: 0.8409 (p0) REVERT: A 954 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8719 (tptp) REVERT: A 1014 MET cc_start: 0.7555 (mtt) cc_final: 0.7350 (mmm) REVERT: A 1072 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.5977 (t80) REVERT: A 1074 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8236 (mttt) REVERT: A 1089 VAL cc_start: 0.6982 (OUTLIER) cc_final: 0.6660 (t) REVERT: A 1131 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7228 (mp) REVERT: B 6 MET cc_start: 0.8967 (mmt) cc_final: 0.8390 (mmt) REVERT: B 8 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8896 (ptp90) REVERT: B 173 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8450 (mtmm) REVERT: B 360 GLN cc_start: 0.8705 (mp10) cc_final: 0.8456 (mp10) REVERT: C 149 MET cc_start: 0.9043 (ttp) cc_final: 0.8750 (ptm) REVERT: C 275 ASP cc_start: 0.8411 (m-30) cc_final: 0.8112 (m-30) REVERT: C 278 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7867 (mm) REVERT: C 326 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8664 (tm-30) REVERT: C 350 MET cc_start: 0.6768 (mpp) cc_final: 0.6547 (mpp) REVERT: C 385 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4470 (pp) REVERT: C 389 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8243 (ttp-110) REVERT: C 427 MET cc_start: 0.8382 (mmm) cc_final: 0.8109 (mmt) REVERT: C 510 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7679 (tt) REVERT: C 803 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8197 (mm) outliers start: 48 outliers final: 28 residues processed: 137 average time/residue: 0.1610 time to fit residues: 34.9683 Evaluate side-chains 135 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 965 ARG Chi-restraints excluded: chain A residue 1072 PHE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 803 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 174 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS B 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.082170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.057982 restraints weight = 61507.368| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.78 r_work: 0.2835 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21495 Z= 0.123 Angle : 0.531 12.456 29312 Z= 0.284 Chirality : 0.040 0.297 3215 Planarity : 0.004 0.043 3517 Dihedral : 18.362 178.623 3460 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.95 % Favored : 95.79 % Rotamer: Outliers : 2.07 % Allowed : 20.61 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2377 helix: 1.84 (0.15), residues: 1127 sheet: -1.05 (0.29), residues: 318 loop : -1.15 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 373 TYR 0.016 0.001 TYR B 690 PHE 0.016 0.001 PHE C 317 TRP 0.009 0.001 TRP A1096 HIS 0.005 0.001 HIS C 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (21495) covalent geometry : angle 0.53097 / 0.28 (29312) hydrogen bonds : bond 0.03496 / 2.29 ( 949) hydrogen bonds : angle 4.25629 / 3.00 ( 2708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 0.901 Fit side-chains REVERT: A 108 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8211 (mp10) REVERT: A 240 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: A 309 LYS cc_start: 0.9176 (ttmt) cc_final: 0.8931 (tppt) REVERT: A 385 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8025 (pp) REVERT: A 784 ASN cc_start: 0.8676 (t0) cc_final: 0.8428 (p0) REVERT: A 788 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8305 (mtm-85) REVERT: A 954 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8718 (tptp) REVERT: A 1072 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.5977 (t80) REVERT: A 1074 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8289 (mttt) REVERT: A 1089 VAL cc_start: 0.6970 (OUTLIER) cc_final: 0.6636 (t) REVERT: A 1131 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7321 (mp) REVERT: B 8 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8896 (ptp90) REVERT: B 173 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8493 (mtmm) REVERT: B 360 GLN cc_start: 0.8696 (mp10) cc_final: 0.8446 (mp10) REVERT: B 680 MET cc_start: 0.9149 (mtm) cc_final: 0.8711 (mtm) REVERT: C 149 MET cc_start: 0.9046 (ttp) cc_final: 0.8756 (ptm) REVERT: C 275 ASP cc_start: 0.8419 (m-30) cc_final: 0.8109 (m-30) REVERT: C 326 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8636 (tm-30) REVERT: C 350 MET cc_start: 0.6795 (mpp) cc_final: 0.6589 (mpp) REVERT: C 385 LEU cc_start: 0.5043 (OUTLIER) cc_final: 0.4483 (pp) REVERT: C 389 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8222 (ttp-110) REVERT: C 510 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7717 (tt) REVERT: C 803 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8197 (mm) outliers start: 43 outliers final: 28 residues processed: 134 average time/residue: 0.1591 time to fit residues: 33.9001 Evaluate side-chains 134 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 965 ARG Chi-restraints excluded: chain A residue 1072 PHE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 803 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 143 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 239 optimal weight: 40.0000 chunk 80 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 241 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 633 HIS ** 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 = 0.3531 r_free = 0.3531 target = 0.080712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056544 restraints weight = 61511.029| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.75 r_work: 0.2792 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21495 Z= 0.218 Angle : 0.576 8.557 29312 Z= 0.306 Chirality : 0.043 0.300 3215 Planarity : 0.004 0.042 3517 Dihedral : 18.401 179.172 3460 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.54 % Favored : 95.20 % Rotamer: Outliers : 2.31 % Allowed : 20.65 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2377 helix: 1.78 (0.15), residues: 1128 sheet: -1.11 (0.29), residues: 318 loop : -1.20 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 195 TYR 0.024 0.002 TYR C 44 PHE 0.019 0.002 PHE B 673 TRP 0.010 0.001 TRP A 897 HIS 0.007 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (21495) covalent geometry : angle 0.57599 / 0.31 (29312) hydrogen bonds : bond 0.03943 / 2.59 ( 949) hydrogen bonds : angle 4.37153 / 3.09 ( 2708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 0.718 Fit side-chains REVERT: A 240 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: A 309 LYS cc_start: 0.9204 (ttmt) cc_final: 0.8963 (tppt) REVERT: A 385 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8242 (pp) REVERT: A 954 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8726 (tptp) REVERT: A 1072 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.5958 (t80) REVERT: A 1074 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8270 (mttp) REVERT: A 1089 VAL cc_start: 0.7055 (OUTLIER) cc_final: 0.6773 (t) REVERT: A 1091 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7152 (tp) REVERT: B 8 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8918 (ptp90) REVERT: B 173 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8574 (mtmm) REVERT: B 360 GLN cc_start: 0.8666 (mp10) cc_final: 0.8435 (mp10) REVERT: B 588 MET cc_start: 0.8571 (tpt) cc_final: 0.8347 (tpt) REVERT: B 680 MET cc_start: 0.9116 (mtm) cc_final: 0.8690 (mtm) REVERT: C 149 MET cc_start: 0.9052 (ttp) cc_final: 0.8733 (ptm) REVERT: C 275 ASP cc_start: 0.8379 (m-30) cc_final: 0.8082 (m-30) REVERT: C 385 LEU cc_start: 0.5179 (OUTLIER) cc_final: 0.3434 (pp) REVERT: C 510 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7728 (tt) REVERT: C 803 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8185 (mm) outliers start: 48 outliers final: 28 residues processed: 135 average time/residue: 0.1527 time to fit residues: 32.3164 Evaluate side-chains 127 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 965 ARG Chi-restraints excluded: chain A residue 1072 PHE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 803 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 67 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 214 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 690 ASN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 284 ASN ** B 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.081717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.057635 restraints weight = 61353.254| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.77 r_work: 0.2823 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21495 Z= 0.128 Angle : 0.543 9.856 29312 Z= 0.290 Chirality : 0.040 0.303 3215 Planarity : 0.004 0.042 3517 Dihedral : 18.368 178.577 3460 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.16 % Favored : 95.58 % Rotamer: Outliers : 1.93 % Allowed : 21.09 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2377 helix: 1.81 (0.15), residues: 1129 sheet: -1.09 (0.29), residues: 318 loop : -1.12 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 389 TYR 0.017 0.001 TYR B 690 PHE 0.020 0.001 PHE C 387 TRP 0.009 0.001 TRP A1096 HIS 0.005 0.001 HIS C 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21495) covalent geometry : angle 0.54311 / 0.29 (29312) hydrogen bonds : bond 0.03599 / 2.35 ( 949) hydrogen bonds : angle 4.28831 / 3.03 ( 2708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4860.69 seconds wall clock time: 84 minutes 15.60 seconds (5055.60 seconds total)