Starting phenix.real_space_refine on Fri Jan 24 00:41:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ixm_60973/01_2025/9ixm_60973.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ixm_60973/01_2025/9ixm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ixm_60973/01_2025/9ixm_60973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ixm_60973/01_2025/9ixm_60973.map" model { file = "/net/cci-nas-00/data/ceres_data/9ixm_60973/01_2025/9ixm_60973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ixm_60973/01_2025/9ixm_60973.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, '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: 11.75, per 1000 atoms: 0.56 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: 5.00 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 6.39 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: 9.67 Time building geometry restraints manager: 5.86 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=" CA GLU B 407 " pdb=" C GLU B 407 " ideal model delta sigma weight residual 1.524 1.575 -0.051 1.26e-02 6.30e+03 1.65e+01 bond pdb=" CA PRO B 408 " pdb=" C PRO B 408 " ideal model delta sigma weight residual 1.520 1.464 0.055 1.42e-02 4.96e+03 1.51e+01 bond pdb=" C ASN B 99 " pdb=" O ASN B 99 " ideal model delta sigma weight residual 1.235 1.198 0.037 1.02e-02 9.61e+03 1.29e+01 bond pdb=" CA GLU A 430 " pdb=" C GLU A 430 " ideal model delta sigma weight residual 1.519 1.483 0.036 1.19e-02 7.06e+03 9.21e+00 bond pdb=" CA LEU C 377 " pdb=" C LEU C 377 " ideal model delta sigma weight residual 1.525 1.567 -0.041 1.40e-02 5.10e+03 8.75e+00 ... (remaining 21490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.05: 29216 6.05 - 12.11: 82 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: 3172 0.155 - 0.309: 29 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.230 Process input model: 51.380 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 0.075 21495 Z= 0.254 Angle : 0.946 30.274 29312 Z= 0.585 Chirality : 0.056 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 : 16.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (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 TRP 0.015 0.001 TRP C 104 HIS 0.006 0.001 HIS B 633 PHE 0.020 0.001 PHE B 634 TYR 0.024 0.001 TYR A 945 ARG 0.007 0.001 ARG A 106 *********************** 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 : 2.260 Fit side-chains revert: symmetry clash 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: 0.8552 (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: 0.3771 time to fit residues: 78.4902 Evaluate side-chains 115 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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 207 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 201 GLN ** A 972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 HIS B 282 GLN B 319 GLN B 633 HIS C 374 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.081471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.057459 restraints weight = 61520.582| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.74 r_work: 0.2820 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 21495 Z= 0.304 Angle : 0.627 10.191 29312 Z= 0.337 Chirality : 0.042 0.187 3215 Planarity : 0.005 0.083 3517 Dihedral : 18.623 175.109 3508 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.59 % Favored : 95.16 % Rotamer: Outliers : 2.89 % Allowed : 20.75 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2377 helix: 1.45 (0.16), residues: 1126 sheet: -1.38 (0.28), residues: 333 loop : -1.44 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 48 HIS 0.004 0.001 HIS A 455 PHE 0.018 0.002 PHE B 185 TYR 0.022 0.002 TYR B 690 ARG 0.005 0.001 ARG C 114 *********************** 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 166 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 106 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7841 (pp) REVERT: A 622 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7978 (tp-100) REVERT: A 633 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7599 (ptm160) REVERT: A 784 ASN cc_start: 0.8643 (t0) cc_final: 0.8412 (p0) REVERT: A 872 MET cc_start: 0.9035 (mmp) cc_final: 0.8756 (mmp) REVERT: A 1091 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.6978 (tp) REVERT: A 1156 ILE cc_start: 0.7950 (pt) cc_final: 0.7490 (mt) REVERT: C 136 MET cc_start: 0.8551 (mmm) cc_final: 0.8268 (mmm) REVERT: C 149 MET cc_start: 0.9083 (ttp) cc_final: 0.8804 (ptm) REVERT: C 261 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8168 (mm-30) REVERT: C 365 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7400 (m-40) REVERT: C 790 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7730 (t0) REVERT: C 803 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8163 (mm) outliers start: 60 outliers final: 15 residues processed: 160 average time/residue: 0.3801 time to fit residues: 93.4587 Evaluate side-chains 118 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 2.537 ------------------------------------------------------------------------------- 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 622 GLN Chi-restraints excluded: chain A residue 633 ARG Chi-restraints excluded: chain A residue 1091 ILE 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 376 HIS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 365 ASN 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 972 GLN B 103 GLN B 256 HIS B 284 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.080352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.057374 restraints weight = 62318.462| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.87 r_work: 0.2799 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21495 Z= 0.276 Angle : 0.578 8.209 29312 Z= 0.313 Chirality : 0.041 0.170 3215 Planarity : 0.004 0.072 3517 Dihedral : 18.554 173.548 3471 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.42 % Favored : 95.37 % Rotamer: Outliers : 2.55 % Allowed : 20.85 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2377 helix: 1.60 (0.16), residues: 1129 sheet: -1.30 (0.28), residues: 329 loop : -1.35 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 943 HIS 0.004 0.001 HIS C 455 PHE 0.025 0.001 PHE C 141 TYR 0.022 0.001 TYR B 690 ARG 0.007 0.000 ARG C 351 *********************** 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 150 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 97 time to evaluate : 2.299 Fit side-chains REVERT: A 135 MET cc_start: 0.8369 (ttm) cc_final: 0.7884 (tmm) REVERT: A 309 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8956 (tppt) REVERT: A 385 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7983 (pp) REVERT: A 650 MET cc_start: 0.8693 (mmm) cc_final: 0.8428 (mmp) REVERT: A 720 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8726 (ptpt) REVERT: A 1025 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8666 (mt-10) REVERT: B 173 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8261 (mtmm) REVERT: B 564 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8372 (ptp90) REVERT: C 136 MET cc_start: 0.8670 (mmm) cc_final: 0.7880 (mmm) REVERT: C 149 MET cc_start: 0.9064 (ttp) cc_final: 0.8768 (ptm) REVERT: C 261 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8255 (mm-30) REVERT: C 275 ASP cc_start: 0.8486 (m-30) cc_final: 0.8191 (m-30) REVERT: C 278 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7929 (mm) REVERT: C 365 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7268 (m-40) REVERT: C 389 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8300 (ttp-110) REVERT: C 803 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8203 (mm) outliers start: 53 outliers final: 20 residues processed: 146 average time/residue: 0.3440 time to fit residues: 78.8030 Evaluate side-chains 120 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 720 LYS Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 67 MET 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 243 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 261 GLU Chi-restraints excluded: chain C residue 264 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 365 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 200 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.080773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.057080 restraints weight = 63085.464| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.70 r_work: 0.2835 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21495 Z= 0.218 Angle : 0.542 7.943 29312 Z= 0.292 Chirality : 0.039 0.157 3215 Planarity : 0.004 0.052 3517 Dihedral : 18.361 176.751 3460 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.75 % Rotamer: Outliers : 2.65 % Allowed : 20.75 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2377 helix: 1.74 (0.16), residues: 1129 sheet: -1.18 (0.29), residues: 306 loop : -1.27 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 943 HIS 0.004 0.001 HIS C 455 PHE 0.014 0.001 PHE C 397 TYR 0.018 0.001 TYR B 690 ARG 0.003 0.000 ARG C 373 *********************** 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 152 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 97 time to evaluate : 2.425 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8738 (ttm) cc_final: 0.8384 (ttm) REVERT: A 385 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7999 (pp) REVERT: A 788 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8329 (mtm-85) REVERT: A 954 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8731 (tptp) REVERT: A 1014 MET cc_start: 0.7572 (mtt) cc_final: 0.7323 (mmm) REVERT: A 1072 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6037 (t80) REVERT: A 1091 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7115 (tp) REVERT: A 1131 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7275 (mp) REVERT: B 31 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8537 (mmtt) REVERT: B 173 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8483 (mtmm) REVERT: B 680 MET cc_start: 0.9053 (mtm) cc_final: 0.8602 (mtm) REVERT: C 136 MET cc_start: 0.8644 (mmm) cc_final: 0.8424 (mmm) REVERT: C 149 MET cc_start: 0.9033 (ttp) cc_final: 0.8740 (ptm) REVERT: C 261 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: C 275 ASP cc_start: 0.8559 (m-30) cc_final: 0.8141 (m-30) REVERT: C 339 MET cc_start: 0.8301 (tpp) cc_final: 0.7677 (tpt) REVERT: C 350 MET cc_start: 0.6724 (mpp) cc_final: 0.6459 (mpp) REVERT: C 365 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.7136 (m-40) REVERT: C 389 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8270 (ttp-110) REVERT: C 803 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8192 (mm) outliers start: 55 outliers final: 21 residues processed: 144 average time/residue: 0.3751 time to fit residues: 84.4430 Evaluate side-chains 122 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN 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 1091 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 67 MET 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 243 LEU Chi-restraints excluded: chain B residue 367 THR 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 261 GLU 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 519 VAL 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 22 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 217 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 302 GLN B 270 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN B 319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.081194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.057167 restraints weight = 61866.273| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.77 r_work: 0.2812 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21495 Z= 0.240 Angle : 0.538 8.725 29312 Z= 0.290 Chirality : 0.039 0.158 3215 Planarity : 0.004 0.047 3517 Dihedral : 18.314 177.817 3460 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.29 % Favored : 95.46 % Rotamer: Outliers : 2.94 % Allowed : 20.17 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2377 helix: 1.81 (0.16), residues: 1126 sheet: -1.17 (0.29), residues: 323 loop : -1.21 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1096 HIS 0.004 0.001 HIS C 455 PHE 0.014 0.001 PHE C 397 TYR 0.020 0.001 TYR B 690 ARG 0.006 0.000 ARG C 195 *********************** 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 152 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 91 time to evaluate : 2.296 Fit side-chains REVERT: A 23 MET cc_start: 0.8733 (ttm) cc_final: 0.8375 (ttm) REVERT: A 108 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: A 385 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8301 (pp) REVERT: A 413 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8648 (tt0) REVERT: A 788 ARG cc_start: 0.8712 (mtm-85) cc_final: 0.8352 (mtm-85) REVERT: A 954 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8740 (tptp) REVERT: A 1072 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.5942 (t80) REVERT: A 1089 VAL cc_start: 0.6985 (OUTLIER) cc_final: 0.6686 (t) REVERT: A 1091 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7143 (tp) REVERT: A 1109 GLN cc_start: 0.9384 (tm-30) cc_final: 0.9155 (mp10) REVERT: A 1131 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7338 (mp) REVERT: B 31 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8538 (mmtt) REVERT: B 173 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8457 (mtmm) REVERT: B 513 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8323 (mp10) REVERT: C 136 MET cc_start: 0.8625 (mmm) cc_final: 0.8381 (mmm) REVERT: C 149 MET cc_start: 0.9043 (ttp) cc_final: 0.8739 (ptm) REVERT: C 261 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8329 (mm-30) REVERT: C 275 ASP cc_start: 0.8593 (m-30) cc_final: 0.8158 (m-30) REVERT: C 278 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7964 (mm) REVERT: C 350 MET cc_start: 0.6672 (mpp) cc_final: 0.6407 (mpp) REVERT: C 385 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.3556 (pp) REVERT: C 803 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8140 (mm) outliers start: 61 outliers final: 26 residues processed: 145 average time/residue: 0.3513 time to fit residues: 79.9989 Evaluate side-chains 126 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 85 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 413 GLN 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 B residue 31 LYS Chi-restraints excluded: chain B residue 67 MET 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 243 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 513 GLN 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 261 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 93 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.082243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.058235 restraints weight = 61542.611| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.79 r_work: 0.2841 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21495 Z= 0.175 Angle : 0.512 8.333 29312 Z= 0.275 Chirality : 0.038 0.153 3215 Planarity : 0.004 0.044 3517 Dihedral : 18.249 178.915 3460 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.83 % Favored : 95.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2377 helix: 1.89 (0.16), residues: 1129 sheet: -1.03 (0.30), residues: 315 loop : -1.07 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1096 HIS 0.005 0.001 HIS C 455 PHE 0.014 0.001 PHE C 397 TYR 0.015 0.001 TYR B 690 ARG 0.005 0.000 ARG C 195 *********************** 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 144 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8611 (ttm) cc_final: 0.8297 (ttm) REVERT: A 108 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: A 385 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8283 (pp) REVERT: A 413 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8628 (tt0) REVERT: A 954 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8695 (tptp) REVERT: A 1072 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.5779 (t80) REVERT: A 1074 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8281 (mttp) REVERT: A 1089 VAL cc_start: 0.6962 (OUTLIER) cc_final: 0.6662 (t) REVERT: A 1091 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7198 (tp) REVERT: A 1131 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7310 (mp) REVERT: B 31 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8445 (mmtt) REVERT: B 38 PHE cc_start: 0.8758 (m-80) cc_final: 0.8532 (m-80) REVERT: B 173 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8513 (mtmm) REVERT: B 513 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: B 680 MET cc_start: 0.9136 (mtm) cc_final: 0.8644 (mtm) REVERT: C 68 PHE cc_start: 0.9102 (m-80) cc_final: 0.8415 (m-80) REVERT: C 136 MET cc_start: 0.8668 (mmm) cc_final: 0.8423 (mmm) REVERT: C 149 MET cc_start: 0.9037 (ttp) cc_final: 0.8750 (ptm) REVERT: C 261 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8364 (mm-30) REVERT: C 275 ASP cc_start: 0.8599 (m-30) cc_final: 0.8143 (m-30) REVERT: C 278 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7872 (mm) REVERT: C 339 MET cc_start: 0.8367 (tpp) cc_final: 0.7617 (tmm) REVERT: C 350 MET cc_start: 0.6682 (mpp) cc_final: 0.6409 (mpp) REVERT: C 510 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7834 (tt) REVERT: C 803 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8063 (mm) outliers start: 48 outliers final: 25 residues processed: 136 average time/residue: 0.3353 time to fit residues: 72.9859 Evaluate side-chains 132 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 413 GLN 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 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 B residue 31 LYS Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 513 GLN 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 161 MET Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 261 GLU 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 321 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 134 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 200 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.080390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.056249 restraints weight = 61250.903| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.75 r_work: 0.2782 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21495 Z= 0.323 Angle : 0.564 8.377 29312 Z= 0.303 Chirality : 0.041 0.170 3215 Planarity : 0.004 0.043 3517 Dihedral : 18.364 178.587 3460 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.50 % Favored : 95.25 % Rotamer: Outliers : 2.74 % Allowed : 20.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2377 helix: 1.81 (0.16), residues: 1128 sheet: -1.07 (0.29), residues: 323 loop : -1.15 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.005 0.001 HIS A 779 PHE 0.015 0.001 PHE B 673 TYR 0.023 0.002 TYR B 690 ARG 0.004 0.000 ARG C 195 *********************** 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 148 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 91 time to evaluate : 2.264 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8768 (ttm) cc_final: 0.8379 (ttm) REVERT: A 385 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8339 (pp) REVERT: A 851 MET cc_start: 0.8600 (ttm) cc_final: 0.8208 (mtp) REVERT: A 954 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8740 (tptp) REVERT: A 1072 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.5948 (t80) REVERT: A 1074 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8217 (mttp) REVERT: A 1089 VAL cc_start: 0.7064 (OUTLIER) cc_final: 0.6750 (t) REVERT: A 1091 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7163 (tp) REVERT: A 1109 GLN cc_start: 0.9448 (tm-30) cc_final: 0.9151 (mp10) REVERT: A 1131 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7401 (mp) REVERT: B 31 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8586 (mmtt) REVERT: B 173 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8606 (mtmm) REVERT: B 444 MET cc_start: 0.8728 (mmm) cc_final: 0.8471 (mmp) REVERT: B 513 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8350 (mp10) REVERT: B 588 MET cc_start: 0.8546 (tpt) cc_final: 0.8322 (tpt) REVERT: B 680 MET cc_start: 0.9118 (mtm) cc_final: 0.8648 (mtm) REVERT: C 136 MET cc_start: 0.8664 (mmm) cc_final: 0.8412 (mmm) REVERT: C 149 MET cc_start: 0.9038 (ttp) cc_final: 0.8761 (ptt) REVERT: C 261 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8327 (mm-30) REVERT: C 275 ASP cc_start: 0.8612 (m-30) cc_final: 0.8150 (m-30) REVERT: C 278 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7976 (mm) REVERT: C 339 MET cc_start: 0.8425 (tpp) cc_final: 0.7670 (tmm) REVERT: C 350 MET cc_start: 0.6867 (mpp) cc_final: 0.6613 (mpp) REVERT: C 510 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7836 (tt) REVERT: C 803 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8136 (mm) outliers start: 57 outliers final: 27 residues processed: 143 average time/residue: 0.3407 time to fit residues: 77.4443 Evaluate side-chains 127 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 156 GLN 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 1131 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 67 MET 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 367 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 513 GLN 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 261 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 321 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 219 optimal weight: 0.0980 chunk 37 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 239 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.082093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.058054 restraints weight = 61741.684| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.80 r_work: 0.2838 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21495 Z= 0.171 Angle : 0.507 8.275 29312 Z= 0.273 Chirality : 0.038 0.156 3215 Planarity : 0.004 0.044 3517 Dihedral : 18.192 174.824 3460 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.62 % Favored : 96.13 % Rotamer: Outliers : 2.26 % Allowed : 20.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2377 helix: 1.90 (0.16), residues: 1128 sheet: -0.95 (0.29), residues: 323 loop : -1.05 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1096 HIS 0.005 0.001 HIS C 455 PHE 0.015 0.001 PHE C 397 TYR 0.014 0.001 TYR B 690 ARG 0.004 0.000 ARG C 195 *********************** 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 138 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 91 time to evaluate : 2.437 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8597 (ttm) cc_final: 0.8275 (ttm) REVERT: A 136 MET cc_start: 0.9025 (mmm) cc_final: 0.8756 (mmm) REVERT: A 385 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8291 (pp) REVERT: A 413 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: A 788 ARG cc_start: 0.8728 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: A 851 MET cc_start: 0.8359 (ttm) cc_final: 0.8126 (mtp) REVERT: A 865 MET cc_start: 0.9166 (pmm) cc_final: 0.8929 (ptp) REVERT: A 954 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8700 (tptp) REVERT: A 1072 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.5888 (t80) REVERT: A 1074 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8264 (mttp) REVERT: A 1089 VAL cc_start: 0.6966 (OUTLIER) cc_final: 0.6661 (t) REVERT: A 1091 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7220 (tp) REVERT: A 1109 GLN cc_start: 0.9446 (tm-30) cc_final: 0.9147 (mp10) REVERT: A 1131 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7337 (mp) REVERT: B 31 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8357 (mmtt) REVERT: B 38 PHE cc_start: 0.8718 (m-80) cc_final: 0.8504 (m-80) REVERT: B 173 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8656 (mtmm) REVERT: B 444 MET cc_start: 0.8737 (mmm) cc_final: 0.8441 (mmp) REVERT: B 513 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8178 (mp10) REVERT: B 680 MET cc_start: 0.9125 (mtm) cc_final: 0.8678 (mtm) REVERT: C 68 PHE cc_start: 0.9117 (m-80) cc_final: 0.8470 (m-80) REVERT: C 136 MET cc_start: 0.8701 (mmm) cc_final: 0.8466 (mmm) REVERT: C 149 MET cc_start: 0.9029 (ttp) cc_final: 0.8739 (ptt) REVERT: C 261 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8315 (mm-30) REVERT: C 275 ASP cc_start: 0.8617 (m-30) cc_final: 0.8149 (m-30) REVERT: C 278 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7922 (mm) REVERT: C 339 MET cc_start: 0.8304 (tpp) cc_final: 0.7492 (tmm) REVERT: C 350 MET cc_start: 0.6715 (mpp) cc_final: 0.6462 (mpp) REVERT: C 510 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7820 (tt) REVERT: C 803 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8070 (mm) outliers start: 47 outliers final: 26 residues processed: 132 average time/residue: 0.3608 time to fit residues: 75.9727 Evaluate side-chains 128 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 578 VAL 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 B residue 31 LYS Chi-restraints excluded: chain B residue 67 MET 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 282 GLN Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 513 GLN 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 123 LEU 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 261 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 445 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 123 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 182 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3546 r_free = 0.3546 target = 0.081306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.057799 restraints weight = 61333.412| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.84 r_work: 0.2803 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21495 Z= 0.232 Angle : 0.525 8.776 29312 Z= 0.281 Chirality : 0.039 0.157 3215 Planarity : 0.004 0.043 3517 Dihedral : 18.224 175.387 3460 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.29 % Favored : 95.46 % Rotamer: Outliers : 2.26 % Allowed : 20.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2377 helix: 1.90 (0.16), residues: 1128 sheet: -0.94 (0.29), residues: 323 loop : -1.05 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1096 HIS 0.005 0.001 HIS C 455 PHE 0.015 0.001 PHE C 397 TYR 0.018 0.001 TYR B 690 ARG 0.004 0.000 ARG C 195 *********************** 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 137 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 90 time to evaluate : 2.311 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8674 (ttm) cc_final: 0.8317 (ttm) REVERT: A 136 MET cc_start: 0.9020 (mmm) cc_final: 0.8762 (mmm) REVERT: A 385 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8312 (pp) REVERT: A 413 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: A 788 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8346 (mtm-85) REVERT: A 851 MET cc_start: 0.8545 (ttm) cc_final: 0.8298 (mtp) REVERT: A 954 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8721 (tptp) REVERT: A 1072 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6094 (t80) REVERT: A 1089 VAL cc_start: 0.7039 (OUTLIER) cc_final: 0.6744 (t) REVERT: A 1091 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7218 (tp) REVERT: A 1109 GLN cc_start: 0.9467 (tm-30) cc_final: 0.9150 (mp10) REVERT: A 1131 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7349 (mp) REVERT: B 31 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8484 (mttm) REVERT: B 173 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8698 (mtmm) REVERT: B 444 MET cc_start: 0.8739 (mmm) cc_final: 0.8480 (mmp) REVERT: B 513 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8242 (mp10) REVERT: B 680 MET cc_start: 0.9102 (mtm) cc_final: 0.8892 (mtm) REVERT: C 68 PHE cc_start: 0.9121 (m-80) cc_final: 0.8444 (m-80) REVERT: C 72 TRP cc_start: 0.8018 (OUTLIER) cc_final: 0.6536 (t60) REVERT: C 136 MET cc_start: 0.8689 (mmm) cc_final: 0.8444 (mmm) REVERT: C 149 MET cc_start: 0.9047 (ttp) cc_final: 0.8747 (ptt) REVERT: C 261 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8269 (mm-30) REVERT: C 275 ASP cc_start: 0.8617 (m-30) cc_final: 0.8144 (m-30) REVERT: C 278 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7929 (mm) REVERT: C 339 MET cc_start: 0.8355 (tpp) cc_final: 0.7410 (tmm) REVERT: C 350 MET cc_start: 0.6832 (mpp) cc_final: 0.6578 (mpp) REVERT: C 510 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7815 (tt) REVERT: C 803 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8053 (mm) outliers start: 47 outliers final: 28 residues processed: 131 average time/residue: 0.3139 time to fit residues: 66.9117 Evaluate side-chains 134 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 413 GLN 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 883 THR 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 B residue 31 LYS Chi-restraints excluded: chain B residue 67 MET 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 367 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain C residue 72 TRP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 LEU 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 261 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 445 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 42 optimal weight: 0.0670 chunk 16 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 204 optimal weight: 0.0980 chunk 180 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 chunk 156 optimal weight: 0.3980 chunk 198 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.082204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.059074 restraints weight = 60997.629| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.02 r_work: 0.2846 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21495 Z= 0.148 Angle : 0.503 8.971 29312 Z= 0.268 Chirality : 0.038 0.151 3215 Planarity : 0.004 0.045 3517 Dihedral : 18.138 173.496 3460 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.62 % Favored : 96.13 % Rotamer: Outliers : 1.73 % Allowed : 21.38 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2377 helix: 1.97 (0.16), residues: 1131 sheet: -0.88 (0.29), residues: 318 loop : -0.98 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1096 HIS 0.006 0.001 HIS C 455 PHE 0.014 0.001 PHE C 397 TYR 0.012 0.001 TYR A 938 ARG 0.004 0.000 ARG C 195 ********************** 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 124 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7889 (ttp) REVERT: A 23 MET cc_start: 0.8563 (ttm) cc_final: 0.8184 (ttm) REVERT: A 136 MET cc_start: 0.8955 (mmm) cc_final: 0.8660 (mmm) REVERT: A 385 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8283 (pp) REVERT: A 413 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: A 851 MET cc_start: 0.8372 (ttm) cc_final: 0.8125 (mtp) REVERT: A 954 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8696 (tptp) REVERT: A 1072 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6001 (t80) REVERT: A 1089 VAL cc_start: 0.6969 (OUTLIER) cc_final: 0.6637 (t) REVERT: A 1131 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7508 (mp) REVERT: B 31 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8368 (mmtt) REVERT: B 38 PHE cc_start: 0.8730 (m-80) cc_final: 0.8503 (m-80) REVERT: B 173 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8751 (mtmm) REVERT: B 444 MET cc_start: 0.8677 (mmm) cc_final: 0.8383 (mmp) REVERT: B 513 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8213 (mp10) REVERT: C 68 PHE cc_start: 0.9142 (m-80) cc_final: 0.8492 (m-80) REVERT: C 136 MET cc_start: 0.8718 (mmm) cc_final: 0.8472 (mmm) REVERT: C 149 MET cc_start: 0.9044 (ttp) cc_final: 0.8731 (ptt) REVERT: C 261 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8480 (mp0) REVERT: C 275 ASP cc_start: 0.8604 (m-30) cc_final: 0.8137 (m-30) REVERT: C 278 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7832 (mm) REVERT: C 339 MET cc_start: 0.8335 (tpp) cc_final: 0.7388 (tmm) REVERT: C 350 MET cc_start: 0.6749 (mpp) cc_final: 0.6497 (mpp) REVERT: C 510 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7940 (tt) REVERT: C 803 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8076 (mm) outliers start: 36 outliers final: 20 residues processed: 118 average time/residue: 0.3495 time to fit residues: 66.9578 Evaluate side-chains 122 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 578 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 B residue 31 LYS Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 513 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 LEU 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 261 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 278 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 233 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 41 optimal weight: 0.0470 chunk 48 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 633 HIS ** 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 = 0.3541 r_free = 0.3541 target = 0.081078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.057625 restraints weight = 61409.967| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.75 r_work: 0.2811 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21495 Z= 0.219 Angle : 0.522 8.839 29312 Z= 0.279 Chirality : 0.039 0.156 3215 Planarity : 0.004 0.043 3517 Dihedral : 18.179 174.579 3460 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.08 % Favored : 95.67 % Rotamer: Outliers : 2.02 % Allowed : 21.09 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2377 helix: 1.97 (0.16), residues: 1130 sheet: -0.84 (0.29), residues: 323 loop : -0.98 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1096 HIS 0.005 0.001 HIS C 455 PHE 0.019 0.001 PHE C 804 TYR 0.018 0.001 TYR B 690 ARG 0.004 0.000 ARG C 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10155.06 seconds wall clock time: 181 minutes 50.26 seconds (10910.26 seconds total)