Starting phenix.real_space_refine on Thu Nov 20 02:31:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6acj_9593/11_2025/6acj_9593.cif Found real_map, /net/cci-nas-00/data/ceres_data/6acj_9593/11_2025/6acj_9593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6acj_9593/11_2025/6acj_9593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6acj_9593/11_2025/6acj_9593.map" model { file = "/net/cci-nas-00/data/ceres_data/6acj_9593/11_2025/6acj_9593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6acj_9593/11_2025/6acj_9593.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.871 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: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 18987 2.51 5 N 4918 2.21 5 O 5646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29715 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "B" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "C" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8241 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1006} Chain breaks: 5 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Time building chain proxies: 6.10, per 1000 atoms: 0.21 Number of scatterers: 29715 At special positions: 0 Unit cell: (146.52, 176.88, 219.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 164 16.00 O 5646 8.00 N 4918 7.00 C 18987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.02 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.01 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.01 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.02 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.04 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.02 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.01 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.00 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 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: 2.03 Conformation dependent library (CDL) restraints added in 1.3 seconds 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7102 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 43 sheets defined 27.8% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 371 through 375 removed outlier: 4.102A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.553A pdb=" N GLN A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 488 through 492 removed outlier: 4.030A pdb=" N GLN A 492 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 729 through 738 removed outlier: 3.842A pdb=" N ASN A 733 " --> pdb=" O THR A 729 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 848 through 864 Processing helix chain 'A' and resid 880 through 888 removed outlier: 3.620A pdb=" N MET A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 removed outlier: 4.095A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.921A pdb=" N ALA A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 4.480A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 965 removed outlier: 3.515A pdb=" N SER A 964 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1013 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 371 through 377 removed outlier: 3.676A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 488 through 492 removed outlier: 4.082A pdb=" N GLN B 492 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 removed outlier: 3.627A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 738 removed outlier: 3.565A pdb=" N TYR B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 765 Processing helix chain 'B' and resid 798 through 808 Processing helix chain 'B' and resid 848 through 864 Processing helix chain 'B' and resid 880 through 888 Processing helix chain 'B' and resid 901 through 920 Processing helix chain 'B' and resid 927 through 949 removed outlier: 4.601A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 966 removed outlier: 3.825A pdb=" N ARG B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1017 removed outlier: 4.197A pdb=" N VAL B1015 " --> pdb=" O MET B1011 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.851A pdb=" N TYR C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.789A pdb=" N SER C 607 " --> pdb=" O CYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 737 removed outlier: 4.079A pdb=" N ASN C 733 " --> pdb=" O THR C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 764 Processing helix chain 'C' and resid 798 through 806 Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 888 removed outlier: 3.571A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 removed outlier: 4.709A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 4.289A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 removed outlier: 4.035A pdb=" N LEU C 966 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1013 removed outlier: 4.125A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.598A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 63 Processing helix chain 'D' and resid 63 through 81 removed outlier: 3.856A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 102 Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.823A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.596A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 3.926A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 219 through 231 removed outlier: 4.105A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 252 removed outlier: 4.576A pdb=" N LEU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.689A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.653A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.815A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 398 through 413 removed outlier: 4.410A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 4.018A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 466 removed outlier: 4.191A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.009A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.605A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.086A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.545A pdb=" N SER D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.508A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix removed outlier: 3.617A pdb=" N ASN D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 8.267A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 250 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 180 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE A 203 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 182 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 201 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 8.267A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 250 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 194 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 59 removed outlier: 4.079A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 140 removed outlier: 5.543A pdb=" N ALA A 237 " --> pdb=" O VAL A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 306 removed outlier: 3.959A pdb=" N VAL A 583 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 302 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 6.979A pdb=" N GLY A 311 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ASN A 528 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.525A pdb=" N PHE A 387 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AB1, first strand: chain 'A' and resid 650 through 651 removed outlier: 3.696A pdb=" N ILE A 650 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 705 through 710 removed outlier: 3.821A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 705 through 710 removed outlier: 3.821A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A1041 " --> pdb=" O ALA A1038 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 1069 through 1070 removed outlier: 3.705A pdb=" N SER A1105 " --> pdb=" O ALA A1069 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AB7, first strand: chain 'B' and resid 32 through 34 removed outlier: 8.327A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 67 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 254 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 71 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 219 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 55 through 59 removed outlier: 4.327A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 81 through 82 removed outlier: 5.262A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 137 through 141 Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 304 removed outlier: 5.694A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 637 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 312 through 314 removed outlier: 3.955A pdb=" N GLY B 534 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 345 removed outlier: 5.125A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 383 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 500 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 387 " --> pdb=" O VAL B 496 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 657 through 658 Processing sheet with id=AC6, first strand: chain 'B' and resid 700 through 701 removed outlier: 3.608A pdb=" N VAL B1050 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 710 Processing sheet with id=AC8, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AC9, first strand: chain 'B' and resid 1032 through 1033 Processing sheet with id=AD1, first strand: chain 'C' and resid 31 through 34 Processing sheet with id=AD2, first strand: chain 'C' and resid 54 through 59 removed outlier: 4.157A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AD4, first strand: chain 'C' and resid 217 through 222 removed outlier: 6.907A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR C 197 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 87 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 92 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 300 through 301 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 removed outlier: 6.318A pdb=" N GLY C 311 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASN C 528 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 341 through 345 removed outlier: 5.430A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.530A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 540 Processing sheet with id=AE2, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.974A pdb=" N SER C 703 " --> pdb=" O THR C1048 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR C1048 " --> pdb=" O SER C 703 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 705 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C1034 " --> pdb=" O LEU C1045 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 716 through 717 Processing sheet with id=AE4, first strand: chain 'C' and resid 1078 through 1079 Processing sheet with id=AE5, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE6, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.813A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 347 through 350 1047 hydrogen bonds defined for protein. 2919 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.85 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.27: 4901 1.27 - 1.41: 8033 1.41 - 1.56: 17272 1.56 - 1.71: 2 1.71 - 1.85: 232 Bond restraints: 30440 Sorted by residual: bond pdb=" CA THR C 678 " pdb=" C THR C 678 " ideal model delta sigma weight residual 1.523 1.371 0.152 1.34e-02 5.57e+03 1.29e+02 bond pdb=" CA TYR C 677 " pdb=" C TYR C 677 " ideal model delta sigma weight residual 1.523 1.390 0.134 1.34e-02 5.57e+03 9.95e+01 bond pdb=" C ALA C 676 " pdb=" O ALA C 676 " ideal model delta sigma weight residual 1.235 1.121 0.114 1.26e-02 6.30e+03 8.20e+01 bond pdb=" N VAL C 642 " pdb=" CA VAL C 642 " ideal model delta sigma weight residual 1.457 1.352 0.105 1.22e-02 6.72e+03 7.39e+01 bond pdb=" C TYR C 677 " pdb=" O TYR C 677 " ideal model delta sigma weight residual 1.235 1.137 0.099 1.26e-02 6.30e+03 6.13e+01 ... (remaining 30435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 40327 3.58 - 7.16: 972 7.16 - 10.73: 97 10.73 - 14.31: 17 14.31 - 17.89: 3 Bond angle restraints: 41416 Sorted by residual: angle pdb=" CA HIS C 641 " pdb=" C HIS C 641 " pdb=" N VAL C 642 " ideal model delta sigma weight residual 115.29 102.64 12.65 1.18e+00 7.18e-01 1.15e+02 angle pdb=" C GLU C 647 " pdb=" N CYS C 648 " pdb=" CA CYS C 648 " ideal model delta sigma weight residual 121.54 103.65 17.89 1.91e+00 2.74e-01 8.77e+01 angle pdb=" C VAL C 642 " pdb=" CA VAL C 642 " pdb=" CB VAL C 642 " ideal model delta sigma weight residual 111.26 97.40 13.86 1.52e+00 4.33e-01 8.32e+01 angle pdb=" N ILE B 891 " pdb=" CA ILE B 891 " pdb=" C ILE B 891 " ideal model delta sigma weight residual 113.47 104.27 9.20 1.01e+00 9.80e-01 8.30e+01 angle pdb=" O HIS C 641 " pdb=" C HIS C 641 " pdb=" N VAL C 642 " ideal model delta sigma weight residual 122.29 133.67 -11.38 1.40e+00 5.10e-01 6.61e+01 ... (remaining 41411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 17027 18.08 - 36.16: 873 36.16 - 54.25: 140 54.25 - 72.33: 26 72.33 - 90.41: 9 Dihedral angle restraints: 18075 sinusoidal: 7035 harmonic: 11040 Sorted by residual: dihedral pdb=" CA GLU C1074 " pdb=" C GLU C1074 " pdb=" N GLY C1075 " pdb=" CA GLY C1075 " ideal model delta harmonic sigma weight residual -180.00 -113.22 -66.78 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA GLU A1074 " pdb=" C GLU A1074 " pdb=" N GLY A1075 " pdb=" CA GLY A1075 " ideal model delta harmonic sigma weight residual -180.00 -115.07 -64.93 0 5.00e+00 4.00e-02 1.69e+02 dihedral pdb=" CB CYS C 603 " pdb=" SG CYS C 603 " pdb=" SG CYS C 635 " pdb=" CB CYS C 635 " ideal model delta sinusoidal sigma weight residual -86.00 -176.41 90.41 1 1.00e+01 1.00e-02 9.67e+01 ... (remaining 18072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 4534 0.166 - 0.333: 90 0.333 - 0.499: 2 0.499 - 0.666: 1 0.666 - 0.832: 1 Chirality restraints: 4628 Sorted by residual: chirality pdb=" CA TYR C 646 " pdb=" N TYR C 646 " pdb=" C TYR C 646 " pdb=" CB TYR C 646 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" CA TYR C 677 " pdb=" N TYR C 677 " pdb=" C TYR C 677 " pdb=" CB TYR C 677 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CB VAL C 642 " pdb=" CA VAL C 642 " pdb=" CG1 VAL C 642 " pdb=" CG2 VAL C 642 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 4625 not shown) Planarity restraints: 5366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 678 " 0.027 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C THR C 678 " -0.091 2.00e-02 2.50e+03 pdb=" O THR C 678 " 0.035 2.00e-02 2.50e+03 pdb=" N MET C 679 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 677 " -0.017 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR C 677 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR C 677 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 677 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 677 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 677 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR C 677 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR C 677 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 641 " 0.018 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C HIS C 641 " -0.072 2.00e-02 2.50e+03 pdb=" O HIS C 641 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL C 642 " 0.025 2.00e-02 2.50e+03 ... (remaining 5363 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 104 2.36 - 3.00: 16089 3.00 - 3.63: 45193 3.63 - 4.27: 69455 4.27 - 4.90: 110117 Nonbonded interactions: 240958 Sorted by model distance: nonbonded pdb=" OE1 GLU C 647 " pdb=" OG SER C 680 " model vdw 1.731 3.040 nonbonded pdb=" O GLU C 647 " pdb=" CB CYS C 648 " model vdw 1.774 3.440 nonbonded pdb=" O GLY C 655 " pdb=" O THR C 678 " model vdw 1.827 3.040 nonbonded pdb=" CB TYR C 646 " pdb=" CE2 TYR C 677 " model vdw 1.896 3.740 nonbonded pdb=" OG1 THR C 678 " pdb=" N MET C 679 " model vdw 2.034 3.120 ... (remaining 240953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = (chain 'B' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 27.260 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.010 0.152 30481 Z= 0.471 Angle : 1.337 17.888 41498 Z= 0.758 Chirality : 0.069 0.832 4628 Planarity : 0.009 0.078 5366 Dihedral : 11.276 77.450 10850 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.59 % Allowed : 16.76 % Favored : 82.66 % Rotamer: Outliers : 0.61 % Allowed : 3.14 % Favored : 96.26 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 1.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.11), residues: 3754 helix: -2.38 (0.13), residues: 955 sheet: -2.32 (0.23), residues: 452 loop : -3.93 (0.10), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG B 797 TYR 0.062 0.004 TYR C 677 PHE 0.052 0.005 PHE A 837 TRP 0.036 0.004 TRP A 476 HIS 0.021 0.004 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00953 (30440) covalent geometry : angle 1.33456 (41416) SS BOND : bond 0.00943 ( 41) SS BOND : angle 2.15380 ( 82) hydrogen bonds : bond 0.14643 ( 1024) hydrogen bonds : angle 8.60887 ( 2919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 603 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7554 (m-40) cc_final: 0.7324 (m-40) REVERT: A 224 LEU cc_start: 0.7758 (mt) cc_final: 0.7453 (tt) REVERT: A 294 GLU cc_start: 0.7791 (tt0) cc_final: 0.7423 (tm-30) REVERT: A 723 TYR cc_start: 0.8350 (t80) cc_final: 0.8075 (t80) REVERT: A 763 VAL cc_start: 0.8931 (t) cc_final: 0.8603 (p) REVERT: A 801 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 918 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8130 (mp0) REVERT: A 1029 TYR cc_start: 0.6118 (m-10) cc_final: 0.5516 (m-10) REVERT: B 85 ASP cc_start: 0.8671 (m-30) cc_final: 0.8400 (t0) REVERT: B 107 MET cc_start: -0.0275 (mmm) cc_final: -0.0532 (mtt) REVERT: B 144 MET cc_start: 0.7173 (mmm) cc_final: 0.6595 (tpt) REVERT: B 151 MET cc_start: 0.5959 (ptm) cc_final: 0.5696 (ptp) REVERT: B 183 ARG cc_start: 0.7300 (mtt90) cc_final: 0.5516 (mmp80) REVERT: B 230 ASN cc_start: 0.6626 (m-40) cc_final: 0.6396 (m-40) REVERT: B 571 LEU cc_start: 0.9152 (mt) cc_final: 0.8765 (tt) REVERT: B 578 PHE cc_start: 0.8131 (p90) cc_final: 0.7707 (p90) REVERT: B 632 GLN cc_start: 0.2577 (mm110) cc_final: 0.2247 (mm-40) REVERT: B 674 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7123 (pp) REVERT: B 835 GLN cc_start: 0.6976 (tt0) cc_final: 0.6196 (mp10) REVERT: B 901 ASN cc_start: 0.7337 (m-40) cc_final: 0.6904 (t0) REVERT: B 922 THR cc_start: 0.7705 (p) cc_final: 0.7412 (t) REVERT: B 947 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7887 (mp10) REVERT: B 1000 ILE cc_start: 0.8308 (tp) cc_final: 0.7990 (tt) REVERT: B 1043 VAL cc_start: 0.9276 (t) cc_final: 0.8929 (p) REVERT: C 85 ASP cc_start: 0.8160 (m-30) cc_final: 0.7759 (p0) REVERT: C 189 ASN cc_start: 0.8639 (t0) cc_final: 0.8402 (t0) REVERT: C 373 LYS cc_start: 0.8056 (mppt) cc_final: 0.7088 (ttpt) REVERT: C 703 SER cc_start: 0.8575 (t) cc_final: 0.8304 (p) REVERT: C 713 MET cc_start: 0.7894 (ptm) cc_final: 0.7487 (ptm) REVERT: C 895 GLN cc_start: 0.5285 (mt0) cc_final: 0.4685 (mt0) REVERT: C 1012 SER cc_start: 0.8541 (p) cc_final: 0.6453 (p) REVERT: C 1089 ARG cc_start: 0.7575 (tmm160) cc_final: 0.6811 (tpp-160) REVERT: D 383 MET cc_start: 0.2983 (mtm) cc_final: 0.2640 (tpp) REVERT: D 474 MET cc_start: 0.3630 (mmm) cc_final: 0.3042 (mmm) outliers start: 20 outliers final: 7 residues processed: 620 average time/residue: 0.2030 time to fit residues: 199.6616 Evaluate side-chains 342 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 334 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 181 HIS A 589 ASN A 632 GLN A 692 ASN A 737 GLN A 759 ASN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN A 889 ASN A 931 GLN A 935 ASN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN B 70 HIS B 118 ASN B 135 ASN B 759 ASN B 766 GLN ** B 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN B1095 GLN B1101 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 155 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 479 ASN C 632 GLN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 GLN C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN D 24 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN D 239 HIS D 250 ASN D 437 ASN D 526 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.131009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.100535 restraints weight = 110168.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.099524 restraints weight = 76187.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.100699 restraints weight = 59353.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.100808 restraints weight = 48134.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.101136 restraints weight = 44361.125| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30481 Z= 0.189 Angle : 0.812 10.632 41498 Z= 0.435 Chirality : 0.049 0.289 4628 Planarity : 0.006 0.064 5366 Dihedral : 8.247 67.227 4064 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.57 % Favored : 87.16 % Rotamer: Outliers : 0.24 % Allowed : 3.20 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.12), residues: 3754 helix: -0.98 (0.15), residues: 963 sheet: -2.04 (0.22), residues: 504 loop : -3.61 (0.11), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 99 TYR 0.025 0.002 TYR C 689 PHE 0.032 0.002 PHE B 262 TRP 0.015 0.002 TRP D 163 HIS 0.012 0.002 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00401 (30440) covalent geometry : angle 0.80805 (41416) SS BOND : bond 0.00483 ( 41) SS BOND : angle 2.01112 ( 82) hydrogen bonds : bond 0.05049 ( 1024) hydrogen bonds : angle 6.79524 ( 2919) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 489 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8197 (mt) cc_final: 0.7986 (mt) REVERT: A 224 LEU cc_start: 0.7889 (mt) cc_final: 0.7362 (tt) REVERT: A 338 TYR cc_start: 0.5579 (p90) cc_final: 0.5044 (p90) REVERT: A 558 PHE cc_start: 0.7911 (m-10) cc_final: 0.7622 (m-10) REVERT: A 801 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 838 ASN cc_start: 0.8799 (p0) cc_final: 0.8465 (p0) REVERT: A 840 LEU cc_start: 0.8998 (mt) cc_final: 0.8541 (mt) REVERT: A 918 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8447 (mm-30) REVERT: A 947 GLN cc_start: 0.8509 (mm-40) cc_final: 0.7834 (tp40) REVERT: A 967 ASP cc_start: 0.5380 (p0) cc_final: 0.4698 (p0) REVERT: A 1013 GLU cc_start: 0.7955 (tp30) cc_final: 0.7710 (tp30) REVERT: A 1029 TYR cc_start: 0.5698 (m-10) cc_final: 0.5426 (m-10) REVERT: B 54 LEU cc_start: 0.9443 (mp) cc_final: 0.9029 (tt) REVERT: B 107 MET cc_start: 0.0245 (mmm) cc_final: -0.0347 (mtt) REVERT: B 144 MET cc_start: 0.7077 (mmm) cc_final: 0.6773 (tpt) REVERT: B 151 MET cc_start: 0.5538 (ptm) cc_final: 0.5187 (ptp) REVERT: B 230 ASN cc_start: 0.7053 (m-40) cc_final: 0.6729 (m-40) REVERT: B 231 PHE cc_start: 0.8494 (p90) cc_final: 0.8154 (p90) REVERT: B 414 ASP cc_start: 0.8666 (m-30) cc_final: 0.7166 (t70) REVERT: B 571 LEU cc_start: 0.9121 (mt) cc_final: 0.8784 (tt) REVERT: B 709 MET cc_start: 0.7643 (mmm) cc_final: 0.7380 (mmm) REVERT: B 752 ILE cc_start: 0.8754 (mm) cc_final: 0.8288 (mm) REVERT: B 922 THR cc_start: 0.7782 (p) cc_final: 0.7581 (t) REVERT: B 1091 PHE cc_start: 0.7908 (t80) cc_final: 0.7633 (t80) REVERT: C 417 MET cc_start: 0.1562 (tpt) cc_final: 0.0606 (ptt) REVERT: C 554 ASP cc_start: 0.7979 (p0) cc_final: 0.7750 (p0) REVERT: C 766 GLN cc_start: 0.7573 (mt0) cc_final: 0.6979 (mt0) REVERT: C 984 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 1023 ASP cc_start: 0.7091 (t70) cc_final: 0.6885 (t70) REVERT: C 1058 THR cc_start: 0.6285 (p) cc_final: 0.6055 (p) REVERT: D 23 GLU cc_start: 0.3028 (mm-30) cc_final: 0.2688 (tm-30) REVERT: D 56 GLU cc_start: 0.6028 (mm-30) cc_final: 0.5827 (tm-30) REVERT: D 332 MET cc_start: 0.3390 (ttm) cc_final: 0.2720 (tmm) REVERT: D 480 MET cc_start: 0.0720 (ttm) cc_final: 0.0431 (ttm) outliers start: 8 outliers final: 2 residues processed: 492 average time/residue: 0.1894 time to fit residues: 151.6875 Evaluate side-chains 324 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 155 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 303 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 744 GLN B 766 GLN ** B 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN B 895 GLN B 901 ASN B 947 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 937 ASN C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 33 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.133249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.104058 restraints weight = 119832.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.102515 restraints weight = 83778.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.103689 restraints weight = 69150.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.103684 restraints weight = 55818.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.103869 restraints weight = 51556.189| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30481 Z= 0.168 Angle : 0.758 10.222 41498 Z= 0.402 Chirality : 0.048 0.257 4628 Planarity : 0.005 0.064 5366 Dihedral : 7.615 65.732 4064 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.24 % Favored : 86.55 % Rotamer: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.13), residues: 3754 helix: -0.30 (0.16), residues: 952 sheet: -1.91 (0.22), residues: 519 loop : -3.45 (0.11), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 620 TYR 0.023 0.002 TYR A 723 PHE 0.029 0.002 PHE B 837 TRP 0.014 0.001 TRP C 868 HIS 0.016 0.002 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00357 (30440) covalent geometry : angle 0.75164 (41416) SS BOND : bond 0.00547 ( 41) SS BOND : angle 2.28912 ( 82) hydrogen bonds : bond 0.04562 ( 1024) hydrogen bonds : angle 6.37204 ( 2919) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 432 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8281 (mt) cc_final: 0.8029 (mt) REVERT: A 338 TYR cc_start: 0.5823 (p90) cc_final: 0.5470 (p90) REVERT: A 367 TYR cc_start: 0.8273 (m-10) cc_final: 0.8071 (m-10) REVERT: A 397 ILE cc_start: 0.7963 (tp) cc_final: 0.7496 (tp) REVERT: A 755 GLU cc_start: 0.8895 (tt0) cc_final: 0.8689 (tt0) REVERT: A 801 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8035 (mt-10) REVERT: A 838 ASN cc_start: 0.8921 (p0) cc_final: 0.8568 (p0) REVERT: A 918 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8525 (mm-30) REVERT: A 947 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7772 (mm-40) REVERT: A 1091 PHE cc_start: 0.7878 (t80) cc_final: 0.7620 (t80) REVERT: A 1096 ILE cc_start: 0.8960 (tt) cc_final: 0.8757 (tt) REVERT: B 37 MET cc_start: 0.8132 (mmm) cc_final: 0.7804 (tpp) REVERT: B 85 ASP cc_start: 0.8795 (m-30) cc_final: 0.8266 (t70) REVERT: B 144 MET cc_start: 0.7097 (mmm) cc_final: 0.6782 (tpt) REVERT: B 151 MET cc_start: 0.5699 (ptm) cc_final: 0.5251 (ptp) REVERT: B 414 ASP cc_start: 0.8675 (m-30) cc_final: 0.7203 (t70) REVERT: B 502 GLU cc_start: 0.6686 (tt0) cc_final: 0.6109 (mt-10) REVERT: B 571 LEU cc_start: 0.9019 (mt) cc_final: 0.8749 (tt) REVERT: B 722 MET cc_start: 0.7795 (tpp) cc_final: 0.7550 (tpp) REVERT: B 736 LEU cc_start: 0.9037 (mt) cc_final: 0.8811 (tt) REVERT: B 922 THR cc_start: 0.7988 (p) cc_final: 0.7759 (t) REVERT: B 947 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8061 (mp10) REVERT: B 984 GLN cc_start: 0.8587 (tt0) cc_final: 0.8322 (tp40) REVERT: B 1032 MET cc_start: 0.6924 (tpp) cc_final: 0.6585 (tpp) REVERT: C 417 MET cc_start: 0.1935 (tpt) cc_final: 0.0697 (ptt) REVERT: C 766 GLN cc_start: 0.7566 (mt0) cc_final: 0.6998 (mt0) REVERT: C 770 MET cc_start: 0.8621 (mtp) cc_final: 0.8373 (mtp) REVERT: C 984 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7545 (tm-30) REVERT: C 1000 ILE cc_start: 0.8218 (tp) cc_final: 0.7939 (tt) REVERT: D 23 GLU cc_start: 0.3109 (mm-30) cc_final: 0.2814 (tm-30) REVERT: D 56 GLU cc_start: 0.6034 (mm-30) cc_final: 0.5358 (pm20) REVERT: D 152 MET cc_start: -0.1960 (mtp) cc_final: -0.2262 (mtm) REVERT: D 332 MET cc_start: 0.3475 (ttm) cc_final: 0.2537 (tmm) outliers start: 3 outliers final: 0 residues processed: 434 average time/residue: 0.1862 time to fit residues: 132.8853 Evaluate side-chains 309 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 114 optimal weight: 9.9990 chunk 304 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 chunk 228 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 365 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN B 766 GLN ** B 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN B 895 GLN B 901 ASN ** B1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 280 GLN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 GLN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.127807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.095990 restraints weight = 111429.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.095647 restraints weight = 79170.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.096477 restraints weight = 65895.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.096733 restraints weight = 52889.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.096963 restraints weight = 46759.122| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 30481 Z= 0.269 Angle : 0.851 11.968 41498 Z= 0.448 Chirality : 0.050 0.230 4628 Planarity : 0.006 0.057 5366 Dihedral : 7.683 63.307 4064 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.21 % Favored : 84.58 % Rotamer: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.13), residues: 3754 helix: -0.18 (0.16), residues: 960 sheet: -2.01 (0.22), residues: 512 loop : -3.44 (0.11), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 426 TYR 0.028 0.002 TYR C 689 PHE 0.029 0.002 PHE C1092 TRP 0.019 0.002 TRP C 868 HIS 0.021 0.002 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00573 (30440) covalent geometry : angle 0.84469 (41416) SS BOND : bond 0.00691 ( 41) SS BOND : angle 2.42440 ( 82) hydrogen bonds : bond 0.04906 ( 1024) hydrogen bonds : angle 6.46828 ( 2919) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 376 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TYR cc_start: 0.5940 (p90) cc_final: 0.5696 (p90) REVERT: A 558 PHE cc_start: 0.7988 (m-10) cc_final: 0.7730 (m-10) REVERT: A 722 MET cc_start: 0.7573 (mmm) cc_final: 0.7342 (mmm) REVERT: A 755 GLU cc_start: 0.8781 (tt0) cc_final: 0.8549 (tt0) REVERT: A 838 ASN cc_start: 0.9057 (p0) cc_final: 0.8240 (p0) REVERT: A 840 LEU cc_start: 0.9119 (mt) cc_final: 0.8515 (mt) REVERT: A 918 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8527 (mm-30) REVERT: A 947 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8125 (mm-40) REVERT: A 1091 PHE cc_start: 0.8169 (t80) cc_final: 0.7870 (t80) REVERT: B 37 MET cc_start: 0.8198 (mmm) cc_final: 0.7890 (tpp) REVERT: B 46 ILE cc_start: 0.9521 (mt) cc_final: 0.9285 (mt) REVERT: B 107 MET cc_start: 0.0731 (mmt) cc_final: -0.0365 (tmm) REVERT: B 144 MET cc_start: 0.7135 (mmm) cc_final: 0.6783 (tpt) REVERT: B 151 MET cc_start: 0.5814 (ptm) cc_final: 0.5235 (ptp) REVERT: B 231 PHE cc_start: 0.8469 (p90) cc_final: 0.8005 (p90) REVERT: B 414 ASP cc_start: 0.8669 (m-30) cc_final: 0.7168 (t70) REVERT: B 502 GLU cc_start: 0.6963 (tt0) cc_final: 0.6583 (mt-10) REVERT: B 571 LEU cc_start: 0.9066 (mt) cc_final: 0.8696 (tt) REVERT: B 722 MET cc_start: 0.7848 (tpp) cc_final: 0.7627 (tpp) REVERT: B 736 LEU cc_start: 0.9184 (mt) cc_final: 0.8967 (tt) REVERT: B 884 MET cc_start: 0.7131 (mmp) cc_final: 0.6098 (tpp) REVERT: B 922 THR cc_start: 0.8028 (p) cc_final: 0.7741 (t) REVERT: B 947 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8217 (mp10) REVERT: B 984 GLN cc_start: 0.8756 (tt0) cc_final: 0.8452 (tp40) REVERT: B 1032 MET cc_start: 0.6766 (tpp) cc_final: 0.6453 (tpp) REVERT: C 163 TYR cc_start: 0.8799 (t80) cc_final: 0.8267 (t80) REVERT: C 373 LYS cc_start: 0.7919 (mppt) cc_final: 0.6982 (ttpt) REVERT: C 600 ASP cc_start: 0.7201 (t70) cc_final: 0.6671 (t0) REVERT: C 755 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7119 (tm-30) REVERT: C 770 MET cc_start: 0.8750 (mtp) cc_final: 0.8413 (mtp) REVERT: C 837 PHE cc_start: 0.7872 (p90) cc_final: 0.7617 (p90) REVERT: C 984 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7768 (tm-30) REVERT: C 1089 ARG cc_start: 0.7993 (tmm160) cc_final: 0.7115 (tpp-160) outliers start: 2 outliers final: 0 residues processed: 377 average time/residue: 0.1864 time to fit residues: 114.7654 Evaluate side-chains 285 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 315 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 154 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 257 optimal weight: 30.0000 chunk 24 optimal weight: 0.6980 chunk 273 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 GLN ** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN B 877 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 ASN C 835 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN C1095 GLN D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.133339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.102587 restraints weight = 110155.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.101783 restraints weight = 74686.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.103079 restraints weight = 61044.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.103155 restraints weight = 49512.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.103457 restraints weight = 46027.117| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30481 Z= 0.135 Angle : 0.706 10.361 41498 Z= 0.373 Chirality : 0.047 0.220 4628 Planarity : 0.005 0.060 5366 Dihedral : 6.946 65.234 4064 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.11 % Favored : 88.76 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.13), residues: 3754 helix: 0.22 (0.16), residues: 972 sheet: -1.58 (0.23), residues: 497 loop : -3.25 (0.12), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 426 TYR 0.028 0.001 TYR C 689 PHE 0.041 0.002 PHE B1077 TRP 0.015 0.001 TRP D 163 HIS 0.011 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00291 (30440) covalent geometry : angle 0.69990 (41416) SS BOND : bond 0.00455 ( 41) SS BOND : angle 2.22697 ( 82) hydrogen bonds : bond 0.04108 ( 1024) hydrogen bonds : angle 5.95437 ( 2919) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TYR cc_start: 0.5815 (p90) cc_final: 0.5505 (p90) REVERT: A 755 GLU cc_start: 0.8536 (tt0) cc_final: 0.8033 (tp30) REVERT: A 801 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7805 (mt-10) REVERT: A 838 ASN cc_start: 0.8896 (p0) cc_final: 0.8344 (p0) REVERT: A 840 LEU cc_start: 0.9082 (mt) cc_final: 0.8729 (mt) REVERT: A 918 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8328 (mm-30) REVERT: A 947 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7621 (tp-100) REVERT: A 987 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 1015 VAL cc_start: 0.8142 (t) cc_final: 0.7885 (t) REVERT: B 37 MET cc_start: 0.8066 (mmm) cc_final: 0.6984 (tpp) REVERT: B 54 LEU cc_start: 0.9266 (mp) cc_final: 0.8969 (tt) REVERT: B 107 MET cc_start: 0.0112 (mmt) cc_final: -0.0855 (tmm) REVERT: B 144 MET cc_start: 0.7130 (mmm) cc_final: 0.6738 (tpt) REVERT: B 151 MET cc_start: 0.5352 (ptm) cc_final: 0.4887 (ptp) REVERT: B 231 PHE cc_start: 0.8335 (p90) cc_final: 0.7836 (p90) REVERT: B 381 ASN cc_start: 0.7890 (m-40) cc_final: 0.7240 (m-40) REVERT: B 414 ASP cc_start: 0.8611 (m-30) cc_final: 0.7021 (t70) REVERT: B 571 LEU cc_start: 0.8885 (mt) cc_final: 0.8642 (tt) REVERT: B 722 MET cc_start: 0.7581 (tpp) cc_final: 0.7314 (tpp) REVERT: B 922 THR cc_start: 0.7832 (p) cc_final: 0.7548 (t) REVERT: B 947 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7856 (mp10) REVERT: B 984 GLN cc_start: 0.8561 (tt0) cc_final: 0.8271 (tp40) REVERT: B 1032 MET cc_start: 0.6909 (tpp) cc_final: 0.6513 (tpp) REVERT: C 373 LYS cc_start: 0.7983 (mppt) cc_final: 0.7024 (ttpt) REVERT: C 722 MET cc_start: 0.8004 (tpp) cc_final: 0.7741 (tpp) REVERT: C 755 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7357 (tm-30) REVERT: C 837 PHE cc_start: 0.7730 (p90) cc_final: 0.7477 (p90) REVERT: C 984 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7624 (tm-30) REVERT: D 56 GLU cc_start: 0.6229 (mm-30) cc_final: 0.5616 (pm20) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.1861 time to fit residues: 135.8416 Evaluate side-chains 312 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 237 optimal weight: 3.9990 chunk 335 optimal weight: 30.0000 chunk 85 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 296 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 354 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN B 939 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN C 756 GLN C 759 ASN C 766 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.133116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.102561 restraints weight = 108968.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.102559 restraints weight = 78049.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.103139 restraints weight = 55512.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.103408 restraints weight = 49680.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.103674 restraints weight = 45017.078| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30481 Z= 0.138 Angle : 0.705 11.793 41498 Z= 0.369 Chirality : 0.047 0.227 4628 Planarity : 0.005 0.098 5366 Dihedral : 6.698 62.760 4064 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.77 % Favored : 88.09 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.13), residues: 3754 helix: 0.35 (0.17), residues: 970 sheet: -1.40 (0.23), residues: 517 loop : -3.20 (0.12), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 747 TYR 0.019 0.001 TYR A 723 PHE 0.033 0.002 PHE B1077 TRP 0.014 0.001 TRP C 868 HIS 0.011 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00299 (30440) covalent geometry : angle 0.69939 (41416) SS BOND : bond 0.00373 ( 41) SS BOND : angle 2.04641 ( 82) hydrogen bonds : bond 0.04083 ( 1024) hydrogen bonds : angle 5.85831 ( 2919) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TYR cc_start: 0.5711 (p90) cc_final: 0.5419 (p90) REVERT: A 801 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 838 ASN cc_start: 0.8914 (p0) cc_final: 0.8172 (p0) REVERT: A 840 LEU cc_start: 0.9004 (mt) cc_final: 0.8399 (mt) REVERT: A 918 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8359 (mm-30) REVERT: A 947 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7626 (tp-100) REVERT: A 1091 PHE cc_start: 0.7956 (t80) cc_final: 0.7646 (t80) REVERT: B 37 MET cc_start: 0.8291 (mmm) cc_final: 0.7027 (tpp) REVERT: B 107 MET cc_start: -0.0738 (mmt) cc_final: -0.1263 (tmm) REVERT: B 144 MET cc_start: 0.7001 (mmm) cc_final: 0.6614 (tpt) REVERT: B 151 MET cc_start: 0.5426 (ptm) cc_final: 0.4979 (ptp) REVERT: B 231 PHE cc_start: 0.8368 (p90) cc_final: 0.8041 (p90) REVERT: B 414 ASP cc_start: 0.8633 (m-30) cc_final: 0.7126 (t70) REVERT: B 502 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6489 (mt-10) REVERT: B 571 LEU cc_start: 0.8749 (mt) cc_final: 0.8382 (tt) REVERT: B 922 THR cc_start: 0.7781 (p) cc_final: 0.7511 (t) REVERT: B 947 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8313 (mp10) REVERT: B 984 GLN cc_start: 0.8686 (tt0) cc_final: 0.8261 (tp40) REVERT: B 1005 ASN cc_start: 0.8603 (m-40) cc_final: 0.8375 (t0) REVERT: B 1032 MET cc_start: 0.6952 (tpp) cc_final: 0.6463 (tpp) REVERT: C 163 TYR cc_start: 0.8387 (t80) cc_final: 0.8180 (t80) REVERT: C 189 ASN cc_start: 0.8557 (t0) cc_final: 0.8288 (t0) REVERT: C 224 LEU cc_start: 0.7881 (mt) cc_final: 0.6846 (tt) REVERT: C 373 LYS cc_start: 0.8053 (mppt) cc_final: 0.7330 (pttt) REVERT: C 417 MET cc_start: 0.2991 (tpt) cc_final: 0.0882 (ptt) REVERT: C 722 MET cc_start: 0.8185 (tpp) cc_final: 0.7925 (tpp) REVERT: C 755 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7286 (tm-30) REVERT: C 758 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7818 (ttm170) REVERT: C 846 LEU cc_start: 0.8227 (tp) cc_final: 0.7997 (tp) REVERT: C 925 THR cc_start: 0.8440 (m) cc_final: 0.8078 (t) REVERT: C 984 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7573 (tm-30) REVERT: D 56 GLU cc_start: 0.6239 (mm-30) cc_final: 0.5688 (pm20) REVERT: D 323 MET cc_start: 0.1087 (mpp) cc_final: 0.0599 (mpp) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.1815 time to fit residues: 122.3152 Evaluate side-chains 303 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 354 optimal weight: 6.9990 chunk 375 optimal weight: 30.0000 chunk 245 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 305 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 214 ASN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 915 GLN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN A1101 ASN ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN B1088 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 280 GLN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.128387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.099101 restraints weight = 119902.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.097179 restraints weight = 89540.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.097749 restraints weight = 74707.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.098188 restraints weight = 63206.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.098294 restraints weight = 56780.704| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 30481 Z= 0.314 Angle : 0.872 12.621 41498 Z= 0.458 Chirality : 0.050 0.237 4628 Planarity : 0.006 0.059 5366 Dihedral : 7.291 62.041 4064 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.48 % Favored : 84.36 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.13), residues: 3754 helix: -0.09 (0.16), residues: 969 sheet: -1.76 (0.23), residues: 523 loop : -3.34 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1073 TYR 0.026 0.002 TYR B 300 PHE 0.027 0.003 PHE A 153 TRP 0.028 0.002 TRP C 868 HIS 0.020 0.002 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00674 (30440) covalent geometry : angle 0.86498 (41416) SS BOND : bond 0.00803 ( 41) SS BOND : angle 2.65167 ( 82) hydrogen bonds : bond 0.04894 ( 1024) hydrogen bonds : angle 6.43580 ( 2919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7521 (ttt180) cc_final: 0.7211 (ttt-90) REVERT: A 338 TYR cc_start: 0.6141 (p90) cc_final: 0.5867 (p90) REVERT: A 636 LEU cc_start: 0.9138 (tp) cc_final: 0.8866 (tt) REVERT: A 838 ASN cc_start: 0.9114 (p0) cc_final: 0.8214 (p0) REVERT: A 840 LEU cc_start: 0.9154 (mt) cc_final: 0.8327 (mt) REVERT: A 918 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8485 (mm-30) REVERT: A 947 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8184 (mm-40) REVERT: A 1091 PHE cc_start: 0.8044 (t80) cc_final: 0.7837 (t80) REVERT: A 1096 ILE cc_start: 0.9092 (tt) cc_final: 0.8873 (tt) REVERT: B 37 MET cc_start: 0.8334 (mmm) cc_final: 0.7113 (tpp) REVERT: B 107 MET cc_start: 0.0406 (mmt) cc_final: -0.0708 (tmm) REVERT: B 144 MET cc_start: 0.7119 (mmm) cc_final: 0.6759 (tpt) REVERT: B 151 MET cc_start: 0.5806 (ptm) cc_final: 0.4994 (ptp) REVERT: B 161 PHE cc_start: 0.6858 (t80) cc_final: 0.5763 (t80) REVERT: B 231 PHE cc_start: 0.8698 (p90) cc_final: 0.8224 (p90) REVERT: B 383 TYR cc_start: 0.7841 (m-80) cc_final: 0.7467 (m-80) REVERT: B 414 ASP cc_start: 0.8690 (m-30) cc_final: 0.7137 (t70) REVERT: B 502 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6582 (mt-10) REVERT: B 571 LEU cc_start: 0.9030 (mt) cc_final: 0.8608 (tt) REVERT: B 622 TYR cc_start: 0.7449 (t80) cc_final: 0.7120 (t80) REVERT: B 855 TYR cc_start: 0.8111 (m-80) cc_final: 0.7850 (m-80) REVERT: B 922 THR cc_start: 0.7890 (p) cc_final: 0.7657 (t) REVERT: B 947 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8191 (mp10) REVERT: B 984 GLN cc_start: 0.9008 (tt0) cc_final: 0.8620 (tp40) REVERT: B 999 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8407 (tm-30) REVERT: B 1032 MET cc_start: 0.6931 (tpp) cc_final: 0.6543 (tpp) REVERT: B 1043 VAL cc_start: 0.9112 (t) cc_final: 0.8714 (p) REVERT: C 37 MET cc_start: 0.7857 (ttp) cc_final: 0.7590 (ttt) REVERT: C 189 ASN cc_start: 0.8656 (t0) cc_final: 0.8439 (t0) REVERT: C 373 LYS cc_start: 0.7909 (mppt) cc_final: 0.7260 (pttt) REVERT: C 722 MET cc_start: 0.8479 (tpp) cc_final: 0.8243 (tpp) REVERT: C 755 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 770 MET cc_start: 0.8478 (mmm) cc_final: 0.7930 (ttm) REVERT: C 837 PHE cc_start: 0.8092 (p90) cc_final: 0.7818 (p90) REVERT: C 846 LEU cc_start: 0.8720 (tp) cc_final: 0.8480 (tp) REVERT: C 984 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7659 (tm-30) REVERT: C 1021 ARG cc_start: 0.8601 (ptm160) cc_final: 0.8292 (ptm-80) REVERT: C 1032 MET cc_start: 0.6816 (ttm) cc_final: 0.6592 (ttm) REVERT: C 1089 ARG cc_start: 0.8108 (tmm160) cc_final: 0.7324 (tpp-160) REVERT: D 56 GLU cc_start: 0.5980 (mm-30) cc_final: 0.5498 (pm20) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1867 time to fit residues: 108.0929 Evaluate side-chains 269 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 125 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 264 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN B 877 GLN B1095 GLN C 135 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.131862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.101502 restraints weight = 109443.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.100235 restraints weight = 78749.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.101628 restraints weight = 64614.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.101728 restraints weight = 49102.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.102001 restraints weight = 47709.428| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30481 Z= 0.143 Angle : 0.717 11.274 41498 Z= 0.376 Chirality : 0.048 0.233 4628 Planarity : 0.005 0.060 5366 Dihedral : 6.717 63.672 4064 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.32 % Favored : 88.55 % Rotamer: Outliers : 0.03 % Allowed : 0.88 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.13), residues: 3754 helix: 0.32 (0.17), residues: 969 sheet: -1.34 (0.24), residues: 494 loop : -3.10 (0.12), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 887 TYR 0.022 0.001 TYR B 723 PHE 0.027 0.002 PHE C1092 TRP 0.015 0.001 TRP C 868 HIS 0.011 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00310 (30440) covalent geometry : angle 0.71151 (41416) SS BOND : bond 0.00405 ( 41) SS BOND : angle 2.07670 ( 82) hydrogen bonds : bond 0.04117 ( 1024) hydrogen bonds : angle 5.92708 ( 2919) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 838 ASN cc_start: 0.8999 (p0) cc_final: 0.8191 (p0) REVERT: A 840 LEU cc_start: 0.9203 (mt) cc_final: 0.8556 (mt) REVERT: A 947 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7791 (tp-100) REVERT: A 1091 PHE cc_start: 0.8229 (t80) cc_final: 0.7938 (t80) REVERT: B 37 MET cc_start: 0.8262 (mmm) cc_final: 0.6935 (tpp) REVERT: B 107 MET cc_start: -0.0218 (mmt) cc_final: -0.1036 (tmm) REVERT: B 144 MET cc_start: 0.7021 (mmm) cc_final: 0.6595 (tpt) REVERT: B 151 MET cc_start: 0.5597 (ptm) cc_final: 0.4931 (ptp) REVERT: B 231 PHE cc_start: 0.8385 (p90) cc_final: 0.7853 (p90) REVERT: B 414 ASP cc_start: 0.8667 (m-30) cc_final: 0.7070 (t70) REVERT: B 502 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6240 (mt-10) REVERT: B 571 LEU cc_start: 0.8898 (mt) cc_final: 0.8612 (tt) REVERT: B 947 GLN cc_start: 0.8614 (mm-40) cc_final: 0.7947 (mp10) REVERT: B 984 GLN cc_start: 0.8693 (tt0) cc_final: 0.8372 (tp40) REVERT: B 1005 ASN cc_start: 0.8908 (m-40) cc_final: 0.8645 (t0) REVERT: B 1032 MET cc_start: 0.6453 (tpp) cc_final: 0.5992 (tpp) REVERT: B 1043 VAL cc_start: 0.8895 (t) cc_final: 0.8412 (p) REVERT: C 189 ASN cc_start: 0.8593 (t0) cc_final: 0.8289 (t0) REVERT: C 224 LEU cc_start: 0.8120 (mm) cc_final: 0.7037 (tt) REVERT: C 367 TYR cc_start: 0.6455 (m-80) cc_final: 0.4817 (t80) REVERT: C 373 LYS cc_start: 0.8056 (mppt) cc_final: 0.7277 (pttt) REVERT: C 755 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7360 (tm-30) REVERT: C 846 LEU cc_start: 0.8464 (tp) cc_final: 0.8126 (tp) REVERT: C 925 THR cc_start: 0.8293 (m) cc_final: 0.7751 (t) REVERT: C 984 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7749 (tm-30) REVERT: D 56 GLU cc_start: 0.6135 (mm-30) cc_final: 0.5604 (pm20) REVERT: D 270 MET cc_start: 0.3095 (tpt) cc_final: 0.2473 (tpt) REVERT: D 323 MET cc_start: 0.1187 (mpp) cc_final: 0.0526 (mpp) outliers start: 1 outliers final: 1 residues processed: 378 average time/residue: 0.1808 time to fit residues: 113.9898 Evaluate side-chains 286 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 142 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 302 optimal weight: 7.9990 chunk 303 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.129555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.099483 restraints weight = 109579.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.098281 restraints weight = 75118.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.098854 restraints weight = 66736.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.099208 restraints weight = 58791.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.099432 restraints weight = 50247.178| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 30481 Z= 0.212 Angle : 0.762 8.955 41498 Z= 0.400 Chirality : 0.048 0.235 4628 Planarity : 0.005 0.059 5366 Dihedral : 6.828 62.209 4064 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.04 % Favored : 85.78 % Rotamer: Outliers : 0.03 % Allowed : 0.49 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.13), residues: 3754 helix: 0.20 (0.16), residues: 968 sheet: -1.47 (0.24), residues: 506 loop : -3.16 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 996 TYR 0.019 0.002 TYR D 385 PHE 0.028 0.002 PHE B 799 TRP 0.047 0.002 TRP B 619 HIS 0.014 0.002 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00459 (30440) covalent geometry : angle 0.75715 (41416) SS BOND : bond 0.00488 ( 41) SS BOND : angle 2.15116 ( 82) hydrogen bonds : bond 0.04320 ( 1024) hydrogen bonds : angle 6.10606 ( 2919) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 PHE cc_start: 0.8121 (m-10) cc_final: 0.7897 (m-10) REVERT: A 838 ASN cc_start: 0.9016 (p0) cc_final: 0.8237 (p0) REVERT: A 840 LEU cc_start: 0.9389 (mt) cc_final: 0.8629 (mt) REVERT: A 947 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7942 (tp-100) REVERT: A 1091 PHE cc_start: 0.8231 (t80) cc_final: 0.7988 (t80) REVERT: B 37 MET cc_start: 0.8398 (mmm) cc_final: 0.7197 (tpp) REVERT: B 107 MET cc_start: -0.0229 (mmt) cc_final: -0.1015 (tmm) REVERT: B 144 MET cc_start: 0.7031 (mmm) cc_final: 0.6591 (tpt) REVERT: B 151 MET cc_start: 0.5887 (ptm) cc_final: 0.5141 (ptp) REVERT: B 183 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7257 (mtt180) REVERT: B 231 PHE cc_start: 0.8400 (p90) cc_final: 0.7937 (p90) REVERT: B 414 ASP cc_start: 0.8685 (m-30) cc_final: 0.6970 (t70) REVERT: B 502 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6831 (mt-10) REVERT: B 571 LEU cc_start: 0.8882 (mt) cc_final: 0.8439 (tt) REVERT: B 622 TYR cc_start: 0.7056 (t80) cc_final: 0.6817 (t80) REVERT: B 922 THR cc_start: 0.7628 (p) cc_final: 0.7380 (t) REVERT: B 947 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8304 (mp10) REVERT: B 984 GLN cc_start: 0.8729 (tt0) cc_final: 0.8367 (tp40) REVERT: B 1032 MET cc_start: 0.6809 (tpp) cc_final: 0.6077 (tpp) REVERT: B 1043 VAL cc_start: 0.9035 (t) cc_final: 0.8632 (p) REVERT: C 189 ASN cc_start: 0.8640 (t0) cc_final: 0.8435 (t0) REVERT: C 224 LEU cc_start: 0.8083 (mm) cc_final: 0.6898 (tp) REVERT: C 373 LYS cc_start: 0.8039 (mppt) cc_final: 0.7296 (pttt) REVERT: C 679 MET cc_start: 0.7553 (tpp) cc_final: 0.7306 (tpp) REVERT: C 755 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 837 PHE cc_start: 0.7725 (p90) cc_final: 0.7375 (p90) REVERT: C 846 LEU cc_start: 0.8582 (tp) cc_final: 0.8366 (tp) REVERT: C 984 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7670 (tm-30) REVERT: D 56 GLU cc_start: 0.6177 (mm-30) cc_final: 0.5659 (pm20) REVERT: D 114 LYS cc_start: 0.5594 (mppt) cc_final: 0.5361 (mmtp) REVERT: D 323 MET cc_start: 0.1343 (mpp) cc_final: 0.0638 (mpp) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.1881 time to fit residues: 106.4434 Evaluate side-chains 264 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 75 optimal weight: 0.8980 chunk 341 optimal weight: 30.0000 chunk 120 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 354 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.130049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.098253 restraints weight = 109867.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.098219 restraints weight = 73432.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.099411 restraints weight = 57430.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.099604 restraints weight = 43843.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.099875 restraints weight = 42906.783| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30481 Z= 0.190 Angle : 0.754 10.358 41498 Z= 0.394 Chirality : 0.048 0.217 4628 Planarity : 0.005 0.058 5366 Dihedral : 6.777 62.248 4064 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.29 % Favored : 86.57 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.13), residues: 3754 helix: 0.25 (0.16), residues: 965 sheet: -1.42 (0.24), residues: 506 loop : -3.12 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 996 TYR 0.031 0.002 TYR B 855 PHE 0.029 0.002 PHE C1092 TRP 0.035 0.002 TRP B 619 HIS 0.013 0.002 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00413 (30440) covalent geometry : angle 0.74734 (41416) SS BOND : bond 0.00506 ( 41) SS BOND : angle 2.30922 ( 82) hydrogen bonds : bond 0.04220 ( 1024) hydrogen bonds : angle 6.05305 ( 2919) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 PHE cc_start: 0.8112 (m-10) cc_final: 0.7853 (m-10) REVERT: A 947 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7838 (tp-100) REVERT: A 1091 PHE cc_start: 0.8156 (t80) cc_final: 0.7952 (t80) REVERT: B 37 MET cc_start: 0.8376 (mmm) cc_final: 0.7196 (tpp) REVERT: B 107 MET cc_start: -0.0050 (mmt) cc_final: -0.0908 (tmm) REVERT: B 144 MET cc_start: 0.7012 (mmm) cc_final: 0.6589 (tpt) REVERT: B 151 MET cc_start: 0.5715 (ptm) cc_final: 0.5028 (ptp) REVERT: B 231 PHE cc_start: 0.8382 (p90) cc_final: 0.7851 (p90) REVERT: B 414 ASP cc_start: 0.8622 (m-30) cc_final: 0.6870 (t70) REVERT: B 502 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6861 (mt-10) REVERT: B 571 LEU cc_start: 0.8850 (mt) cc_final: 0.8471 (tt) REVERT: B 622 TYR cc_start: 0.7037 (t80) cc_final: 0.6819 (t80) REVERT: B 947 GLN cc_start: 0.8648 (mm-40) cc_final: 0.7942 (mp10) REVERT: B 984 GLN cc_start: 0.8521 (tt0) cc_final: 0.8256 (tp40) REVERT: B 1005 ASN cc_start: 0.8623 (m-40) cc_final: 0.8372 (m-40) REVERT: B 1032 MET cc_start: 0.6813 (tpp) cc_final: 0.6081 (tpp) REVERT: B 1043 VAL cc_start: 0.9050 (t) cc_final: 0.8621 (p) REVERT: C 163 TYR cc_start: 0.8425 (t80) cc_final: 0.7697 (t80) REVERT: C 189 ASN cc_start: 0.8628 (t0) cc_final: 0.8423 (t0) REVERT: C 224 LEU cc_start: 0.8189 (mm) cc_final: 0.7064 (tp) REVERT: C 373 LYS cc_start: 0.8058 (mppt) cc_final: 0.7282 (pttt) REVERT: C 755 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7442 (tm-30) REVERT: C 837 PHE cc_start: 0.7755 (p90) cc_final: 0.7313 (p90) REVERT: C 846 LEU cc_start: 0.8643 (tp) cc_final: 0.8404 (tp) REVERT: C 925 THR cc_start: 0.8296 (m) cc_final: 0.7839 (t) REVERT: C 984 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7567 (tm-30) REVERT: D 56 GLU cc_start: 0.6162 (mm-30) cc_final: 0.5637 (pm20) REVERT: D 114 LYS cc_start: 0.5629 (mppt) cc_final: 0.5386 (mmtp) REVERT: D 323 MET cc_start: 0.1302 (mpp) cc_final: 0.0608 (mpp) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1911 time to fit residues: 107.4349 Evaluate side-chains 271 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 323 optimal weight: 30.0000 chunk 334 optimal weight: 30.0000 chunk 179 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 300 optimal weight: 0.5980 chunk 185 optimal weight: 0.3980 chunk 209 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 135 ASN B 280 GLN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.132453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.101528 restraints weight = 112078.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.101889 restraints weight = 77631.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.102101 restraints weight = 58762.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.102511 restraints weight = 54032.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.102796 restraints weight = 45849.899| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30481 Z= 0.141 Angle : 0.707 10.777 41498 Z= 0.369 Chirality : 0.047 0.193 4628 Planarity : 0.005 0.059 5366 Dihedral : 6.487 63.215 4064 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.85 % Favored : 88.04 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.13), residues: 3754 helix: 0.42 (0.17), residues: 972 sheet: -1.29 (0.24), residues: 507 loop : -3.03 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 996 TYR 0.032 0.001 TYR B 855 PHE 0.020 0.002 PHE A 153 TRP 0.029 0.001 TRP B 619 HIS 0.016 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00308 (30440) covalent geometry : angle 0.70200 (41416) SS BOND : bond 0.00399 ( 41) SS BOND : angle 2.07978 ( 82) hydrogen bonds : bond 0.03965 ( 1024) hydrogen bonds : angle 5.85766 ( 2919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5605.68 seconds wall clock time: 97 minutes 48.57 seconds (5868.57 seconds total)