Starting phenix.real_space_refine on Thu Mar 5 13:35:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0c_22591/03_2026/7k0c_22591.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0c_22591/03_2026/7k0c_22591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0c_22591/03_2026/7k0c_22591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0c_22591/03_2026/7k0c_22591.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0c_22591/03_2026/7k0c_22591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0c_22591/03_2026/7k0c_22591.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 110 5.16 5 C 14198 2.51 5 N 3833 2.21 5 O 4399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22540 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4109 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain: "B" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain: "K" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1737 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "J" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain breaks: 1 Chain: "E" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1785 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain breaks: 1 Chain: "D" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 838 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 2 Chain: "G" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain breaks: 1 Chain: "F" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1773 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.72, per 1000 atoms: 0.25 Number of scatterers: 22540 At special positions: 0 Unit cell: (177.6, 195.6, 128.4, 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 110 16.00 O 4399 8.00 N 3833 7.00 C 14198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS C 46 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 307 " distance=2.04 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 526 " distance=2.05 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS F 414 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.04 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS K 414 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 414 " - pdb=" SG CYS I 414 " distance=2.04 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Simple disulfide: pdb=" SG CYS I 367 " - pdb=" SG CYS I 426 " distance=2.04 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 536 " distance=2.04 Simple disulfide: pdb=" SG CYS J 367 " - pdb=" SG CYS J 426 " distance=2.03 Simple disulfide: pdb=" SG CYS J 414 " - pdb=" SG CYS E 414 " distance=2.03 Simple disulfide: pdb=" SG CYS J 474 " - pdb=" SG CYS J 536 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS G 414 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.02 Simple disulfide: pdb=" SG CYS H 575 " - pdb=" SG CYS G 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.02 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS F 575 " distance=2.01 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 134 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.06 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.05 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 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG M 1 " - " ASN D 49 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5510 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 69 sheets defined 11.4% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 57 through 61 removed outlier: 3.834A pdb=" N ALA C 61 " --> pdb=" O SER C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.716A pdb=" N SER C 87 " --> pdb=" O GLN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.772A pdb=" N ALA C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.610A pdb=" N VAL C 245 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 298 through 302 removed outlier: 4.082A pdb=" N ALA C 302 " --> pdb=" O LYS C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.889A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 392 removed outlier: 4.199A pdb=" N GLU C 392 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.841A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 517 through 521 Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.598A pdb=" N ASN B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 467 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'K' and resid 353 through 361 Processing helix chain 'K' and resid 414 through 420 removed outlier: 4.123A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 466 Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'L' and resid 353 through 361 Processing helix chain 'L' and resid 415 through 421 removed outlier: 3.873A pdb=" N ASN L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY L 421 " --> pdb=" O ASP L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 removed outlier: 3.503A pdb=" N LEU L 464 " --> pdb=" O ALA L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 531 Processing helix chain 'I' and resid 353 through 361 Processing helix chain 'I' and resid 417 through 421 removed outlier: 3.891A pdb=" N GLY I 421 " --> pdb=" O TRP I 418 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 467 removed outlier: 3.607A pdb=" N ARG I 467 " --> pdb=" O GLN I 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 530 Processing helix chain 'J' and resid 353 through 360 Processing helix chain 'J' and resid 525 through 529 Processing helix chain 'E' and resid 353 through 361 removed outlier: 4.256A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.773A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER E 420 " --> pdb=" O ASP E 416 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 465 Processing helix chain 'E' and resid 525 through 529 Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 420 removed outlier: 3.994A pdb=" N TRP H 418 " --> pdb=" O CYS H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 466 Processing helix chain 'H' and resid 525 through 529 Processing helix chain 'H' and resid 553 through 557 removed outlier: 3.927A pdb=" N THR H 556 " --> pdb=" O ASP H 553 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY H 557 " --> pdb=" O LYS H 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 553 through 557' Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'G' and resid 353 through 360 removed outlier: 3.542A pdb=" N LEU G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 removed outlier: 3.796A pdb=" N TRP G 418 " --> pdb=" O CYS G 414 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY G 421 " --> pdb=" O ASP G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 466 removed outlier: 4.088A pdb=" N LEU G 464 " --> pdb=" O ALA G 460 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 498 No H-bonds generated for 'chain 'G' and resid 496 through 498' Processing helix chain 'G' and resid 525 through 529 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 415 through 419 Processing helix chain 'F' and resid 462 through 466 Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 13 removed outlier: 3.645A pdb=" N GLU C 108 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 12 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS C 35 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER C 51 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.436A pdb=" N VAL C 124 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 135 removed outlier: 3.548A pdb=" N VAL C 130 " --> pdb=" O ILE C 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 147 through 151 removed outlier: 6.966A pdb=" N LEU C 147 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 226 through 229 removed outlier: 7.265A pdb=" N LEU C 252 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 234 through 239 Processing sheet with id=AA8, first strand: chain 'C' and resid 340 through 344 removed outlier: 3.616A pdb=" N GLY C 419 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS C 367 " --> pdb=" O TRP C 422 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 424 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP C 366 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 349 through 354 Processing sheet with id=AB1, first strand: chain 'C' and resid 460 through 462 Processing sheet with id=AB2, first strand: chain 'C' and resid 474 through 479 removed outlier: 4.043A pdb=" N GLU C 474 " --> pdb=" O LYS C 529 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY C 522 " --> pdb=" O TYR C 541 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR C 541 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR C 524 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 539 " --> pdb=" O TYR C 524 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N CYS C 526 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR C 537 " --> pdb=" O CYS C 526 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL C 528 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 346 through 350 removed outlier: 5.025A pdb=" N PHE A 405 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 379 through 383 removed outlier: 3.610A pdb=" N THR A 379 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 428 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 437 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 456 through 457 removed outlier: 3.527A pdb=" N VAL A 476 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 517 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AB8, first strand: chain 'A' and resid 567 through 569 removed outlier: 7.248A pdb=" N VAL A 567 " --> pdb=" O TYR D 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.727A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 365 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 381 through 382 Processing sheet with id=AC2, first strand: chain 'B' and resid 455 through 457 removed outlier: 3.661A pdb=" N ALA B 517 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS B 518 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA B 504 " --> pdb=" O HIS B 518 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE B 520 " --> pdb=" O THR B 502 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR B 502 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR B 522 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR B 500 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.507A pdb=" N GLN B 490 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG B 550 " --> pdb=" O CYS B 536 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.518A pdb=" N VAL L 567 " --> pdb=" O LEU K 566 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU L 566 " --> pdb=" O VAL I 567 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 346 through 350 removed outlier: 6.079A pdb=" N THR K 366 " --> pdb=" O ALA K 411 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA K 411 " --> pdb=" O THR K 366 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU K 368 " --> pdb=" O GLY K 409 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLY K 409 " --> pdb=" O LEU K 368 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N THR K 370 " --> pdb=" O ALA K 407 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA K 407 " --> pdb=" O THR K 370 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 379 through 383 removed outlier: 3.683A pdb=" N THR K 379 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS K 426 " --> pdb=" O GLN K 439 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN K 439 " --> pdb=" O CYS K 426 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 455 through 457 removed outlier: 3.902A pdb=" N LEU K 475 " --> pdb=" O TYR K 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 455 through 457 removed outlier: 3.902A pdb=" N LEU K 475 " --> pdb=" O TYR K 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 493 through 494 removed outlier: 3.736A pdb=" N THR K 535 " --> pdb=" O MET K 489 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 346 through 348 Processing sheet with id=AD2, first strand: chain 'L' and resid 379 through 382 removed outlier: 3.552A pdb=" N ILE L 441 " --> pdb=" O PHE L 424 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 455 through 457 removed outlier: 3.522A pdb=" N LEU L 457 " --> pdb=" O THR L 473 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL L 501 " --> pdb=" O ILE L 520 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 493 through 494 removed outlier: 3.808A pdb=" N ARG L 550 " --> pdb=" O CYS L 536 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR L 548 " --> pdb=" O VAL L 538 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 506 through 507 Processing sheet with id=AD6, first strand: chain 'I' and resid 347 through 348 Processing sheet with id=AD7, first strand: chain 'I' and resid 364 through 365 removed outlier: 3.546A pdb=" N LEU I 365 " --> pdb=" O ALA I 411 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 411 " --> pdb=" O LEU I 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'I' and resid 381 through 383 removed outlier: 4.275A pdb=" N SER I 381 " --> pdb=" O THR I 427 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR I 427 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE I 424 " --> pdb=" O ILE I 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE I 441 " --> pdb=" O PHE I 424 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 455 through 457 removed outlier: 3.851A pdb=" N THR I 473 " --> pdb=" O LEU I 457 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE I 472 " --> pdb=" O LEU I 521 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 493 through 494 Processing sheet with id=AE2, first strand: chain 'I' and resid 506 through 507 Processing sheet with id=AE3, first strand: chain 'J' and resid 348 through 350 removed outlier: 3.619A pdb=" N PHE J 348 " --> pdb=" O LEU J 368 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR J 366 " --> pdb=" O ILE J 350 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 424 through 427 removed outlier: 3.657A pdb=" N PHE J 424 " --> pdb=" O ILE J 441 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN J 439 " --> pdb=" O CYS J 426 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 455 through 457 removed outlier: 3.845A pdb=" N THR J 473 " --> pdb=" O LEU J 457 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR J 477 " --> pdb=" O ALA J 517 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA J 517 " --> pdb=" O THR J 477 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE J 479 " --> pdb=" O TYR J 515 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 455 through 457 removed outlier: 3.845A pdb=" N THR J 473 " --> pdb=" O LEU J 457 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 493 through 494 removed outlier: 3.538A pdb=" N GLN J 487 " --> pdb=" O VAL J 537 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 566 through 567 Processing sheet with id=AE9, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.854A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 379 through 383 Processing sheet with id=AF2, first strand: chain 'E' and resid 455 through 457 removed outlier: 3.559A pdb=" N LEU E 457 " --> pdb=" O THR E 473 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 501 " --> pdb=" O ILE E 520 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 469 through 471 removed outlier: 3.815A pdb=" N VAL E 523 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AF5, first strand: chain 'H' and resid 364 through 369 removed outlier: 3.714A pdb=" N LEU H 365 " --> pdb=" O ALA H 411 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA H 411 " --> pdb=" O LEU H 365 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA H 407 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR H 404 " --> pdb=" O HIS H 400 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU H 398 " --> pdb=" O SER H 406 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL H 408 " --> pdb=" O ILE H 396 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE H 396 " --> pdb=" O VAL H 408 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 379 through 383 removed outlier: 4.455A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR H 429 " --> pdb=" O THR H 379 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 469 through 473 Processing sheet with id=AF8, first strand: chain 'H' and resid 476 through 479 removed outlier: 5.146A pdb=" N THR H 477 " --> pdb=" O ALA H 517 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA H 517 " --> pdb=" O THR H 477 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE H 479 " --> pdb=" O TYR H 515 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AG1, first strand: chain 'D' and resid 9 through 11 Processing sheet with id=AG2, first strand: chain 'D' and resid 21 through 22 removed outlier: 8.226A pdb=" N ASN F 563 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG D 36 " --> pdb=" O ASN F 563 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.720A pdb=" N VAL D 42 " --> pdb=" O VAL F 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AG5, first strand: chain 'G' and resid 364 through 370 removed outlier: 3.611A pdb=" N CYS G 367 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 409 " --> pdb=" O CYS G 367 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 379 through 380 removed outlier: 4.036A pdb=" N THR G 379 " --> pdb=" O THR G 429 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 383 through 384 Processing sheet with id=AG8, first strand: chain 'G' and resid 455 through 457 removed outlier: 4.004A pdb=" N CYS G 474 " --> pdb=" O SER G 519 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER G 519 " --> pdb=" O CYS G 474 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AH1, first strand: chain 'G' and resid 506 through 507 Processing sheet with id=AH2, first strand: chain 'F' and resid 349 through 350 removed outlier: 3.605A pdb=" N ALA F 411 " --> pdb=" O LEU F 365 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 381 through 383 removed outlier: 3.584A pdb=" N VAL F 428 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 437 " --> pdb=" O VAL F 428 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS F 430 " --> pdb=" O SER F 435 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER F 435 " --> pdb=" O HIS F 430 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 456 through 457 removed outlier: 3.611A pdb=" N SER F 519 " --> pdb=" O CYS F 474 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 485 through 488 Processing sheet with id=AH6, first strand: chain 'F' and resid 506 through 507 562 hydrogen bonds defined for protein. 1341 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: 3.52 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3774 1.32 - 1.45: 6372 1.45 - 1.58: 12802 1.58 - 1.71: 1 1.71 - 1.85: 141 Bond restraints: 23090 Sorted by residual: bond pdb=" C MET A 506 " pdb=" N PRO A 507 " ideal model delta sigma weight residual 1.332 1.482 -0.150 1.33e-02 5.65e+03 1.27e+02 bond pdb=" C PRO B 505 " pdb=" O PRO B 505 " ideal model delta sigma weight residual 1.235 1.183 0.052 1.30e-02 5.92e+03 1.63e+01 bond pdb=" CB VAL B 567 " pdb=" CG1 VAL B 567 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.25e+00 bond pdb=" CB VAL G 567 " pdb=" CG1 VAL G 567 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.11e+00 bond pdb=" CA ALA B 517 " pdb=" CB ALA B 517 " ideal model delta sigma weight residual 1.532 1.488 0.043 1.56e-02 4.11e+03 7.68e+00 ... (remaining 23085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 30949 2.96 - 5.91: 553 5.91 - 8.87: 51 8.87 - 11.82: 11 11.82 - 14.78: 7 Bond angle restraints: 31571 Sorted by residual: angle pdb=" C MET A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.89 131.39 -11.50 1.02e+00 9.61e-01 1.27e+02 angle pdb=" C VAL B 501 " pdb=" N THR B 502 " pdb=" CA THR B 502 " ideal model delta sigma weight residual 122.99 114.16 8.83 1.41e+00 5.03e-01 3.92e+01 angle pdb=" CA CYS G 536 " pdb=" CB CYS G 536 " pdb=" SG CYS G 536 " ideal model delta sigma weight residual 114.40 128.62 -14.22 2.30e+00 1.89e-01 3.82e+01 angle pdb=" CA CYS G 474 " pdb=" CB CYS G 474 " pdb=" SG CYS G 474 " ideal model delta sigma weight residual 114.40 128.09 -13.69 2.30e+00 1.89e-01 3.54e+01 angle pdb=" N MET A 506 " pdb=" CA MET A 506 " pdb=" CB MET A 506 " ideal model delta sigma weight residual 110.37 119.96 -9.59 1.78e+00 3.16e-01 2.90e+01 ... (remaining 31566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 12650 18.01 - 36.03: 1185 36.03 - 54.04: 151 54.04 - 72.05: 30 72.05 - 90.06: 14 Dihedral angle restraints: 14030 sinusoidal: 5549 harmonic: 8481 Sorted by residual: dihedral pdb=" CB CYS C 253 " pdb=" SG CYS C 253 " pdb=" SG CYS C 261 " pdb=" CB CYS C 261 " ideal model delta sinusoidal sigma weight residual 93.00 14.36 78.64 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS F 367 " pdb=" SG CYS F 367 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual 93.00 166.72 -73.72 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS L 414 " pdb=" SG CYS L 414 " pdb=" SG CYS I 414 " pdb=" CB CYS I 414 " ideal model delta sinusoidal sigma weight residual -86.00 -159.15 73.15 1 1.00e+01 1.00e-02 6.82e+01 ... (remaining 14027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3074 0.076 - 0.152: 567 0.152 - 0.229: 34 0.229 - 0.305: 6 0.305 - 0.381: 2 Chirality restraints: 3683 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.49e+00 chirality pdb=" CA VAL B 501 " pdb=" N VAL B 501 " pdb=" C VAL B 501 " pdb=" CB VAL B 501 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA ARG K 514 " pdb=" N ARG K 514 " pdb=" C ARG K 514 " pdb=" CB ARG K 514 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 3680 not shown) Planarity restraints: 4057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 443 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO I 444 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO I 444 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO I 444 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 488 " 0.028 2.00e-02 2.50e+03 2.71e-02 1.83e+01 pdb=" CG TRP G 488 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP G 488 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP G 488 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 488 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP G 488 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 488 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 488 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 488 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 488 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 42 " -0.064 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO D 43 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO D 43 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 43 " -0.053 5.00e-02 4.00e+02 ... (remaining 4054 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 431 2.53 - 3.12: 19850 3.12 - 3.72: 36888 3.72 - 4.31: 49179 4.31 - 4.90: 77083 Nonbonded interactions: 183431 Sorted by model distance: nonbonded pdb=" OD1 ASP B 453 " pdb=" OG1 THR B 477 " model vdw 1.940 3.040 nonbonded pdb=" O THR I 533 " pdb=" OG1 THR I 551 " model vdw 2.021 3.040 nonbonded pdb=" OG SER K 524 " pdb=" OE1 GLU K 527 " model vdw 2.044 3.040 nonbonded pdb=" OG SER B 381 " pdb=" OG1 THR B 427 " model vdw 2.045 3.040 nonbonded pdb=" O GLU G 526 " pdb=" OG1 THR G 530 " model vdw 2.052 3.040 ... (remaining 183426 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 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'E' and (resid 345 through 442 or (resid 443 and (name N or name CA or na \ me C or name O or name CB )) or resid 444 or resid 449 through 512 or (resid 513 \ and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 through 512 or (resid \ 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'G' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'I' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'J' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 12 or (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 442 or (resid 443 and (name N \ or name CA or name C or name O or name CB )) or resid 444 or resid 449 through 5 \ 68)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 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: 0.050 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.470 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 0.008 0.150 23128 Z= 0.346 Angle : 1.019 14.781 31649 Z= 0.545 Chirality : 0.056 0.381 3683 Planarity : 0.007 0.125 4056 Dihedral : 13.561 90.064 8412 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 33.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.07 % Favored : 84.93 % Rotamer: Outliers : 0.12 % Allowed : 0.70 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.35 (0.15), residues: 2860 helix: -3.09 (0.29), residues: 183 sheet: -1.86 (0.15), residues: 1084 loop : -2.40 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG G 384 TYR 0.043 0.003 TYR H 534 PHE 0.029 0.003 PHE C 237 TRP 0.072 0.003 TRP G 488 HIS 0.009 0.002 HIS H 400 Details of bonding type rmsd covalent geometry : bond 0.00758 (23090) covalent geometry : angle 1.01410 (31571) SS BOND : bond 0.00998 ( 36) SS BOND : angle 2.12576 ( 72) hydrogen bonds : bond 0.30950 ( 557) hydrogen bonds : angle 10.98295 ( 1341) link_BETA1-4 : bond 0.00963 ( 1) link_BETA1-4 : angle 4.14435 ( 3) link_NAG-ASN : bond 0.00561 ( 1) link_NAG-ASN : angle 3.21369 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 426 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 LEU cc_start: 0.8893 (mm) cc_final: 0.8639 (mt) REVERT: C 176 ASP cc_start: 0.7922 (m-30) cc_final: 0.7339 (t0) REVERT: C 326 LEU cc_start: 0.8673 (tp) cc_final: 0.8346 (tp) REVERT: C 382 ASP cc_start: 0.8033 (p0) cc_final: 0.7469 (p0) REVERT: C 470 PHE cc_start: 0.8947 (m-80) cc_final: 0.8035 (m-80) REVERT: C 511 LEU cc_start: 0.6418 (pp) cc_final: 0.5757 (tp) REVERT: A 380 ILE cc_start: 0.7949 (mp) cc_final: 0.7699 (mm) REVERT: A 549 GLU cc_start: 0.8349 (pp20) cc_final: 0.7857 (tm-30) REVERT: B 410 GLU cc_start: 0.6753 (pp20) cc_final: 0.6406 (pp20) REVERT: B 423 ARG cc_start: 0.8646 (tmm160) cc_final: 0.7124 (ttm110) REVERT: B 490 GLN cc_start: 0.8575 (pp30) cc_final: 0.8011 (pp30) REVERT: B 525 GLU cc_start: 0.8287 (pp20) cc_final: 0.7887 (pm20) REVERT: K 487 GLN cc_start: 0.7565 (pp30) cc_final: 0.7288 (pp30) REVERT: L 346 ARG cc_start: 0.5918 (pmt170) cc_final: 0.5701 (ptt180) REVERT: L 418 TRP cc_start: 0.6362 (t-100) cc_final: 0.5462 (t-100) REVERT: I 453 ASP cc_start: 0.8503 (p0) cc_final: 0.8173 (p0) REVERT: I 506 MET cc_start: 0.8662 (mpp) cc_final: 0.8254 (mpp) REVERT: J 489 MET cc_start: 0.6647 (mpp) cc_final: 0.5886 (mpp) REVERT: J 534 TYR cc_start: 0.8152 (m-10) cc_final: 0.7869 (m-10) REVERT: E 346 ARG cc_start: 0.7271 (mmp80) cc_final: 0.6482 (mmm160) REVERT: E 357 ILE cc_start: 0.7646 (pt) cc_final: 0.7444 (pt) REVERT: E 455 TYR cc_start: 0.6801 (m-80) cc_final: 0.6572 (m-80) REVERT: H 489 MET cc_start: 0.8709 (mmp) cc_final: 0.8460 (tpp) REVERT: D 50 ILE cc_start: 0.8667 (tp) cc_final: 0.8300 (tt) REVERT: G 346 ARG cc_start: 0.6098 (mpp80) cc_final: 0.4908 (ttt180) REVERT: G 453 ASP cc_start: 0.8118 (p0) cc_final: 0.7168 (p0) REVERT: G 455 TYR cc_start: 0.7294 (m-80) cc_final: 0.6217 (m-80) REVERT: G 490 GLN cc_start: 0.8684 (pp30) cc_final: 0.8420 (pp30) REVERT: G 549 GLU cc_start: 0.8500 (tt0) cc_final: 0.8211 (tt0) REVERT: F 417 ASP cc_start: 0.8749 (m-30) cc_final: 0.8519 (m-30) REVERT: F 514 ARG cc_start: 0.8682 (mtt180) cc_final: 0.8298 (mtt180) outliers start: 3 outliers final: 0 residues processed: 428 average time/residue: 0.1621 time to fit residues: 103.7160 Evaluate side-chains 307 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN C 426 ASN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN K 439 GLN K 450 HIS ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 493 GLN ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 ASN ** J 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** 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 = 0.4418 r_free = 0.4418 target = 0.137945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.101353 restraints weight = 60446.704| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 4.37 r_work: 0.3750 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 23128 Z= 0.213 Angle : 0.849 17.273 31649 Z= 0.436 Chirality : 0.051 0.228 3683 Planarity : 0.006 0.092 4056 Dihedral : 7.131 52.955 3156 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 1.83 % Allowed : 12.78 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.15 (0.15), residues: 2860 helix: -3.02 (0.26), residues: 210 sheet: -1.66 (0.15), residues: 1095 loop : -2.28 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 451 TYR 0.025 0.002 TYR H 455 PHE 0.020 0.002 PHE B 424 TRP 0.026 0.002 TRP F 488 HIS 0.007 0.001 HIS K 430 Details of bonding type rmsd covalent geometry : bond 0.00477 (23090) covalent geometry : angle 0.84603 (31571) SS BOND : bond 0.01147 ( 36) SS BOND : angle 1.49635 ( 72) hydrogen bonds : bond 0.05950 ( 557) hydrogen bonds : angle 8.50996 ( 1341) link_BETA1-4 : bond 0.00122 ( 1) link_BETA1-4 : angle 2.75690 ( 3) link_NAG-ASN : bond 0.00793 ( 1) link_NAG-ASN : angle 2.94631 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 390 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 TYR cc_start: 0.7569 (m-80) cc_final: 0.6836 (m-80) REVERT: C 176 ASP cc_start: 0.8003 (m-30) cc_final: 0.7385 (t0) REVERT: C 326 LEU cc_start: 0.8416 (tp) cc_final: 0.8077 (tp) REVERT: C 366 TRP cc_start: 0.7905 (t-100) cc_final: 0.6437 (t60) REVERT: C 382 ASP cc_start: 0.7944 (p0) cc_final: 0.7611 (p0) REVERT: C 470 PHE cc_start: 0.9097 (m-80) cc_final: 0.8028 (m-80) REVERT: C 511 LEU cc_start: 0.6725 (pp) cc_final: 0.6116 (tp) REVERT: A 549 GLU cc_start: 0.8076 (pp20) cc_final: 0.7793 (tm-30) REVERT: B 410 GLU cc_start: 0.6850 (pp20) cc_final: 0.6500 (pp20) REVERT: B 423 ARG cc_start: 0.8652 (tmm160) cc_final: 0.6974 (mtm-85) REVERT: B 490 GLN cc_start: 0.8490 (pp30) cc_final: 0.8076 (pp30) REVERT: B 506 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.8027 (mtm) REVERT: K 487 GLN cc_start: 0.7844 (pp30) cc_final: 0.7448 (pp30) REVERT: L 418 TRP cc_start: 0.6684 (t-100) cc_final: 0.5800 (t-100) REVERT: I 414 CYS cc_start: 0.7427 (p) cc_final: 0.7026 (p) REVERT: I 416 ASP cc_start: 0.8683 (p0) cc_final: 0.8261 (p0) REVERT: I 453 ASP cc_start: 0.9026 (p0) cc_final: 0.8395 (p0) REVERT: I 500 TYR cc_start: 0.6366 (p90) cc_final: 0.6010 (p90) REVERT: E 346 ARG cc_start: 0.7774 (mmp80) cc_final: 0.6938 (ttt-90) REVERT: E 453 ASP cc_start: 0.8498 (t0) cc_final: 0.7900 (t0) REVERT: E 455 TYR cc_start: 0.7709 (m-80) cc_final: 0.6963 (m-80) REVERT: E 568 MET cc_start: 0.6928 (pmm) cc_final: 0.6247 (pmm) REVERT: H 489 MET cc_start: 0.8716 (mmp) cc_final: 0.8507 (tpp) REVERT: H 526 GLU cc_start: 0.8548 (mp0) cc_final: 0.8095 (pm20) REVERT: H 527 GLU cc_start: 0.8375 (mp0) cc_final: 0.8131 (mp0) REVERT: H 534 TYR cc_start: 0.8559 (m-80) cc_final: 0.7920 (m-10) REVERT: D 70 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6781 (pttt) REVERT: G 453 ASP cc_start: 0.8488 (p0) cc_final: 0.7976 (p0) REVERT: G 456 LEU cc_start: 0.8257 (tp) cc_final: 0.7833 (tp) REVERT: G 483 ASP cc_start: 0.8216 (t0) cc_final: 0.8014 (t0) REVERT: G 499 LYS cc_start: 0.9064 (mppt) cc_final: 0.8755 (mtmm) REVERT: G 553 ASP cc_start: 0.7539 (t70) cc_final: 0.7146 (t70) REVERT: F 515 TYR cc_start: 0.8358 (m-80) cc_final: 0.7924 (m-10) REVERT: F 568 MET cc_start: 0.8098 (mmt) cc_final: 0.7804 (mmt) outliers start: 47 outliers final: 33 residues processed: 416 average time/residue: 0.1576 time to fit residues: 100.4524 Evaluate side-chains 354 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 319 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain J residue 386 ASN Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 472 ILE Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 522 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 556 THR Chi-restraints excluded: chain F residue 567 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 157 optimal weight: 0.0030 chunk 69 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 249 optimal weight: 40.0000 chunk 63 optimal weight: 5.9990 overall best weight: 3.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 439 GLN ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.136463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.099298 restraints weight = 60772.844| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 4.42 r_work: 0.3700 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 23128 Z= 0.264 Angle : 0.835 16.848 31649 Z= 0.427 Chirality : 0.050 0.216 3683 Planarity : 0.006 0.073 4056 Dihedral : 7.014 49.432 3156 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 3.93 % Allowed : 17.18 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.03 (0.15), residues: 2860 helix: -2.82 (0.27), residues: 200 sheet: -1.65 (0.15), residues: 1082 loop : -2.17 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 467 TYR 0.022 0.002 TYR C 228 PHE 0.016 0.002 PHE K 358 TRP 0.037 0.002 TRP F 488 HIS 0.009 0.001 HIS H 400 Details of bonding type rmsd covalent geometry : bond 0.00601 (23090) covalent geometry : angle 0.83116 (31571) SS BOND : bond 0.00963 ( 36) SS BOND : angle 1.62800 ( 72) hydrogen bonds : bond 0.05382 ( 557) hydrogen bonds : angle 8.15025 ( 1341) link_BETA1-4 : bond 0.00724 ( 1) link_BETA1-4 : angle 2.84643 ( 3) link_NAG-ASN : bond 0.00543 ( 1) link_NAG-ASN : angle 3.52960 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 353 time to evaluate : 0.726 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: C 23 TYR cc_start: 0.7724 (m-80) cc_final: 0.7076 (m-80) REVERT: C 176 ASP cc_start: 0.8008 (m-30) cc_final: 0.7319 (t0) REVERT: C 326 LEU cc_start: 0.8512 (tp) cc_final: 0.8198 (tp) REVERT: C 382 ASP cc_start: 0.8074 (p0) cc_final: 0.7814 (p0) REVERT: C 398 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7960 (pp) REVERT: C 470 PHE cc_start: 0.9102 (m-80) cc_final: 0.8029 (m-80) REVERT: C 511 LEU cc_start: 0.6768 (pp) cc_final: 0.6168 (tp) REVERT: A 528 TRP cc_start: 0.8690 (OUTLIER) cc_final: 0.8454 (t60) REVERT: B 410 GLU cc_start: 0.6811 (pp20) cc_final: 0.6430 (pp20) REVERT: B 423 ARG cc_start: 0.8687 (tmm160) cc_final: 0.6904 (mtm-85) REVERT: B 490 GLN cc_start: 0.8647 (pp30) cc_final: 0.8164 (pp30) REVERT: B 506 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8015 (mtm) REVERT: L 418 TRP cc_start: 0.6576 (t-100) cc_final: 0.5550 (t-100) REVERT: I 375 TYR cc_start: 0.8317 (t80) cc_final: 0.7933 (t80) REVERT: I 414 CYS cc_start: 0.7368 (p) cc_final: 0.6887 (p) REVERT: I 416 ASP cc_start: 0.8704 (p0) cc_final: 0.8189 (p0) REVERT: I 453 ASP cc_start: 0.9060 (p0) cc_final: 0.8330 (p0) REVERT: I 500 TYR cc_start: 0.6409 (p90) cc_final: 0.6103 (p90) REVERT: J 491 ARG cc_start: 0.8515 (mtt90) cc_final: 0.7972 (mpp80) REVERT: E 346 ARG cc_start: 0.7853 (mmp80) cc_final: 0.6924 (ttt-90) REVERT: E 451 ARG cc_start: 0.7871 (mmt-90) cc_final: 0.7456 (mmt-90) REVERT: E 453 ASP cc_start: 0.8440 (t0) cc_final: 0.7765 (t0) REVERT: E 455 TYR cc_start: 0.7732 (m-80) cc_final: 0.6966 (m-80) REVERT: E 533 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8876 (m) REVERT: H 467 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7639 (mmm-85) REVERT: H 534 TYR cc_start: 0.8621 (m-10) cc_final: 0.7924 (m-10) REVERT: G 453 ASP cc_start: 0.8697 (p0) cc_final: 0.8246 (p0) REVERT: G 489 MET cc_start: 0.8462 (mmm) cc_final: 0.8076 (tmm) REVERT: G 491 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7644 (mmm-85) REVERT: G 499 LYS cc_start: 0.9083 (mppt) cc_final: 0.8800 (mtmm) REVERT: G 553 ASP cc_start: 0.7607 (t70) cc_final: 0.7222 (t70) REVERT: F 506 MET cc_start: 0.9000 (mpp) cc_final: 0.8784 (mpp) REVERT: F 515 TYR cc_start: 0.8572 (m-80) cc_final: 0.8099 (m-10) REVERT: F 550 ARG cc_start: 0.8057 (ttm110) cc_final: 0.7805 (ttm110) outliers start: 101 outliers final: 66 residues processed: 420 average time/residue: 0.1535 time to fit residues: 100.9990 Evaluate side-chains 397 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 327 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain J residue 386 ASN Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 472 ILE Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 HIS Chi-restraints excluded: chain J residue 522 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain G residue 419 ASN Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 536 CYS Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 556 THR Chi-restraints excluded: chain F residue 567 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 275 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 400 HIS ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.138314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.101645 restraints weight = 60750.905| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 4.51 r_work: 0.3743 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23128 Z= 0.186 Angle : 0.769 18.028 31649 Z= 0.390 Chirality : 0.048 0.226 3683 Planarity : 0.006 0.060 4056 Dihedral : 6.602 47.004 3156 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 4.32 % Allowed : 19.36 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.15), residues: 2860 helix: -2.81 (0.27), residues: 220 sheet: -1.48 (0.15), residues: 1058 loop : -2.12 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 491 TYR 0.021 0.002 TYR K 375 PHE 0.028 0.002 PHE B 424 TRP 0.026 0.002 TRP F 488 HIS 0.008 0.001 HIS H 400 Details of bonding type rmsd covalent geometry : bond 0.00425 (23090) covalent geometry : angle 0.76651 (31571) SS BOND : bond 0.00689 ( 36) SS BOND : angle 1.42308 ( 72) hydrogen bonds : bond 0.04528 ( 557) hydrogen bonds : angle 7.70879 ( 1341) link_BETA1-4 : bond 0.00624 ( 1) link_BETA1-4 : angle 2.62275 ( 3) link_NAG-ASN : bond 0.00607 ( 1) link_NAG-ASN : angle 2.83582 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 376 time to evaluate : 0.753 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: C 23 TYR cc_start: 0.7712 (m-80) cc_final: 0.7135 (m-80) REVERT: C 176 ASP cc_start: 0.7994 (m-30) cc_final: 0.7304 (t0) REVERT: C 326 LEU cc_start: 0.8458 (tp) cc_final: 0.8124 (tp) REVERT: C 382 ASP cc_start: 0.8042 (p0) cc_final: 0.7697 (p0) REVERT: C 398 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7895 (pp) REVERT: C 470 PHE cc_start: 0.9050 (m-80) cc_final: 0.7957 (m-80) REVERT: C 476 TYR cc_start: 0.7127 (p90) cc_final: 0.6677 (p90) REVERT: C 511 LEU cc_start: 0.6755 (pp) cc_final: 0.6074 (tp) REVERT: A 376 ASP cc_start: 0.8026 (m-30) cc_final: 0.7475 (t70) REVERT: B 410 GLU cc_start: 0.6803 (pp20) cc_final: 0.6293 (pp20) REVERT: B 423 ARG cc_start: 0.8640 (tmm160) cc_final: 0.6930 (mtm-85) REVERT: B 490 GLN cc_start: 0.8552 (pp30) cc_final: 0.8064 (pp30) REVERT: L 475 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8567 (tp) REVERT: I 375 TYR cc_start: 0.8251 (t80) cc_final: 0.7916 (t80) REVERT: I 414 CYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7140 (p) REVERT: I 416 ASP cc_start: 0.8690 (p0) cc_final: 0.8067 (p0) REVERT: I 439 GLN cc_start: 0.6118 (mt0) cc_final: 0.5872 (mt0) REVERT: I 453 ASP cc_start: 0.9053 (p0) cc_final: 0.8284 (p0) REVERT: I 500 TYR cc_start: 0.6354 (p90) cc_final: 0.6120 (p90) REVERT: J 488 TRP cc_start: 0.7824 (m-10) cc_final: 0.7436 (m-10) REVERT: J 489 MET cc_start: 0.6366 (mpp) cc_final: 0.5370 (mpp) REVERT: J 514 ARG cc_start: 0.7948 (mmt90) cc_final: 0.7644 (mmt90) REVERT: E 346 ARG cc_start: 0.7878 (mmp80) cc_final: 0.6922 (ttt-90) REVERT: E 451 ARG cc_start: 0.7856 (mmt-90) cc_final: 0.7492 (mmt-90) REVERT: E 453 ASP cc_start: 0.8383 (t0) cc_final: 0.7713 (t0) REVERT: E 455 TYR cc_start: 0.7661 (m-80) cc_final: 0.6906 (m-80) REVERT: E 533 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8832 (m) REVERT: H 364 LYS cc_start: 0.6185 (tptt) cc_final: 0.5866 (tptt) REVERT: H 483 ASP cc_start: 0.7657 (t0) cc_final: 0.7312 (t0) REVERT: H 508 GLU cc_start: 0.8085 (tp30) cc_final: 0.7740 (tp30) REVERT: H 534 TYR cc_start: 0.8580 (m-10) cc_final: 0.7897 (m-10) REVERT: G 453 ASP cc_start: 0.8577 (p0) cc_final: 0.8176 (p0) REVERT: G 489 MET cc_start: 0.8467 (mmm) cc_final: 0.8174 (tmm) REVERT: G 499 LYS cc_start: 0.9065 (mppt) cc_final: 0.8824 (mtmm) REVERT: G 518 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.6847 (m90) REVERT: G 553 ASP cc_start: 0.7565 (t70) cc_final: 0.7148 (t70) REVERT: G 568 MET cc_start: 0.8510 (ttp) cc_final: 0.8299 (mtm) REVERT: F 515 TYR cc_start: 0.8530 (m-80) cc_final: 0.8039 (m-10) outliers start: 111 outliers final: 67 residues processed: 453 average time/residue: 0.1546 time to fit residues: 109.2932 Evaluate side-chains 406 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 334 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 558 LYS Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 414 CYS Chi-restraints excluded: chain I residue 474 CYS Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 518 HIS Chi-restraints excluded: chain J residue 386 ASN Chi-restraints excluded: chain J residue 428 VAL Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 472 ILE Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 HIS Chi-restraints excluded: chain J residue 522 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain H residue 353 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 419 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 536 CYS Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 567 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 219 optimal weight: 0.0670 chunk 145 optimal weight: 0.7980 chunk 157 optimal weight: 0.0000 chunk 274 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 239 optimal weight: 0.6980 overall best weight: 0.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 400 HIS I 490 GLN ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.142107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.106819 restraints weight = 59742.388| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 5.06 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23128 Z= 0.134 Angle : 0.747 18.088 31649 Z= 0.372 Chirality : 0.047 0.233 3683 Planarity : 0.005 0.054 4056 Dihedral : 6.124 45.453 3156 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.86 % Allowed : 21.15 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.15), residues: 2860 helix: -2.49 (0.29), residues: 215 sheet: -1.22 (0.15), residues: 1051 loop : -1.92 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 394 TYR 0.019 0.001 TYR K 375 PHE 0.020 0.001 PHE F 354 TRP 0.032 0.002 TRP L 418 HIS 0.014 0.001 HIS G 518 Details of bonding type rmsd covalent geometry : bond 0.00298 (23090) covalent geometry : angle 0.74270 (31571) SS BOND : bond 0.00685 ( 36) SS BOND : angle 1.62134 ( 72) hydrogen bonds : bond 0.04094 ( 557) hydrogen bonds : angle 7.31342 ( 1341) link_BETA1-4 : bond 0.00264 ( 1) link_BETA1-4 : angle 2.80652 ( 3) link_NAG-ASN : bond 0.00771 ( 1) link_NAG-ASN : angle 2.36982 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 391 time to evaluate : 0.867 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: C 23 TYR cc_start: 0.7204 (m-80) cc_final: 0.6606 (m-80) REVERT: C 176 ASP cc_start: 0.7866 (m-30) cc_final: 0.7302 (t0) REVERT: C 326 LEU cc_start: 0.8364 (tp) cc_final: 0.8086 (tp) REVERT: C 366 TRP cc_start: 0.7765 (t-100) cc_final: 0.6508 (t-100) REVERT: C 382 ASP cc_start: 0.7990 (p0) cc_final: 0.7617 (p0) REVERT: C 398 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7721 (pp) REVERT: C 470 PHE cc_start: 0.8973 (m-80) cc_final: 0.8071 (m-80) REVERT: C 511 LEU cc_start: 0.6369 (pp) cc_final: 0.6051 (tp) REVERT: A 376 ASP cc_start: 0.7876 (m-30) cc_final: 0.7283 (t70) REVERT: B 410 GLU cc_start: 0.7065 (pp20) cc_final: 0.6542 (pp20) REVERT: B 487 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: B 489 MET cc_start: 0.7559 (tpp) cc_final: 0.7351 (tpp) REVERT: B 490 GLN cc_start: 0.8216 (pp30) cc_final: 0.7934 (pp30) REVERT: K 487 GLN cc_start: 0.7474 (pt0) cc_final: 0.7146 (pt0) REVERT: I 375 TYR cc_start: 0.7833 (t80) cc_final: 0.7548 (t80) REVERT: I 414 CYS cc_start: 0.6418 (OUTLIER) cc_final: 0.6022 (p) REVERT: I 416 ASP cc_start: 0.8619 (p0) cc_final: 0.8059 (p0) REVERT: I 453 ASP cc_start: 0.8768 (p0) cc_final: 0.8111 (p0) REVERT: I 489 MET cc_start: 0.7920 (tpp) cc_final: 0.7600 (tpp) REVERT: I 508 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6480 (tm-30) REVERT: J 464 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8137 (pp) REVERT: J 489 MET cc_start: 0.6761 (mpp) cc_final: 0.5722 (mpp) REVERT: E 346 ARG cc_start: 0.7881 (mmp80) cc_final: 0.7101 (ttt-90) REVERT: E 451 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7351 (mmt-90) REVERT: E 453 ASP cc_start: 0.8129 (t0) cc_final: 0.7624 (t0) REVERT: H 364 LYS cc_start: 0.6398 (tptt) cc_final: 0.6167 (tptt) REVERT: H 508 GLU cc_start: 0.7991 (tp30) cc_final: 0.7753 (tp30) REVERT: H 534 TYR cc_start: 0.8514 (m-10) cc_final: 0.7761 (m-10) REVERT: G 453 ASP cc_start: 0.8120 (p0) cc_final: 0.7467 (p0) REVERT: G 456 LEU cc_start: 0.7582 (tp) cc_final: 0.7380 (tp) REVERT: G 518 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7179 (m90) REVERT: G 553 ASP cc_start: 0.7493 (t70) cc_final: 0.7202 (t70) REVERT: F 385 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: F 515 TYR cc_start: 0.8453 (m-80) cc_final: 0.8044 (m-10) REVERT: F 546 ARG cc_start: 0.8853 (mpp80) cc_final: 0.8174 (mmt180) outliers start: 99 outliers final: 62 residues processed: 461 average time/residue: 0.1458 time to fit residues: 106.0914 Evaluate side-chains 417 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 348 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 414 CYS Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 518 HIS Chi-restraints excluded: chain J residue 386 ASN Chi-restraints excluded: chain J residue 428 VAL Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 472 ILE Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 HIS Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain H residue 353 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 419 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain F residue 385 GLN Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 113 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 281 optimal weight: 9.9990 chunk 220 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 239 optimal weight: 0.4980 chunk 199 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 463 GLN ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.141017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.105202 restraints weight = 59689.214| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 5.00 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23128 Z= 0.151 Angle : 0.757 16.713 31649 Z= 0.378 Chirality : 0.048 0.261 3683 Planarity : 0.005 0.059 4056 Dihedral : 6.048 45.768 3156 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.25 % Allowed : 21.50 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.15), residues: 2860 helix: -2.46 (0.30), residues: 208 sheet: -1.16 (0.15), residues: 1063 loop : -1.83 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 491 TYR 0.018 0.001 TYR K 375 PHE 0.024 0.001 PHE B 424 TRP 0.046 0.002 TRP F 488 HIS 0.008 0.001 HIS G 518 Details of bonding type rmsd covalent geometry : bond 0.00347 (23090) covalent geometry : angle 0.75127 (31571) SS BOND : bond 0.00536 ( 36) SS BOND : angle 2.01000 ( 72) hydrogen bonds : bond 0.04060 ( 557) hydrogen bonds : angle 7.24456 ( 1341) link_BETA1-4 : bond 0.00828 ( 1) link_BETA1-4 : angle 2.56015 ( 3) link_NAG-ASN : bond 0.00735 ( 1) link_NAG-ASN : angle 2.53332 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 375 time to evaluate : 0.725 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: C 23 TYR cc_start: 0.7299 (m-80) cc_final: 0.6677 (m-80) REVERT: C 176 ASP cc_start: 0.7868 (m-30) cc_final: 0.7383 (t0) REVERT: C 326 LEU cc_start: 0.8414 (tp) cc_final: 0.8131 (tp) REVERT: C 382 ASP cc_start: 0.8026 (p0) cc_final: 0.7666 (p0) REVERT: C 398 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7737 (pp) REVERT: C 412 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8473 (pt0) REVERT: C 511 LEU cc_start: 0.6497 (pp) cc_final: 0.6120 (tp) REVERT: A 376 ASP cc_start: 0.7784 (m-30) cc_final: 0.7251 (t70) REVERT: A 530 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 388 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: B 410 GLU cc_start: 0.6982 (pp20) cc_final: 0.6469 (pp20) REVERT: B 423 ARG cc_start: 0.8450 (tmm160) cc_final: 0.6835 (ttm110) REVERT: B 487 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: B 490 GLN cc_start: 0.8358 (pp30) cc_final: 0.7828 (pp30) REVERT: K 487 GLN cc_start: 0.7557 (pt0) cc_final: 0.7322 (pt0) REVERT: L 475 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8416 (tp) REVERT: L 489 MET cc_start: 0.7452 (mmp) cc_final: 0.7004 (mmp) REVERT: I 375 TYR cc_start: 0.7703 (t80) cc_final: 0.7414 (t80) REVERT: I 414 CYS cc_start: 0.6417 (OUTLIER) cc_final: 0.6135 (p) REVERT: I 416 ASP cc_start: 0.8618 (p0) cc_final: 0.8055 (p0) REVERT: I 453 ASP cc_start: 0.8809 (p0) cc_final: 0.8175 (p0) REVERT: I 489 MET cc_start: 0.7653 (tpp) cc_final: 0.7379 (tpp) REVERT: I 508 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6531 (tm-30) REVERT: J 489 MET cc_start: 0.6787 (mpp) cc_final: 0.5751 (mpp) REVERT: E 451 ARG cc_start: 0.7778 (mmt-90) cc_final: 0.7348 (mmt-90) REVERT: E 453 ASP cc_start: 0.8162 (t0) cc_final: 0.7617 (t0) REVERT: H 364 LYS cc_start: 0.6244 (tptt) cc_final: 0.5990 (tptt) REVERT: H 488 TRP cc_start: 0.8449 (m100) cc_final: 0.8033 (m100) REVERT: H 508 GLU cc_start: 0.7847 (tp30) cc_final: 0.7411 (tp30) REVERT: H 534 TYR cc_start: 0.8524 (m-10) cc_final: 0.7752 (m-10) REVERT: G 453 ASP cc_start: 0.8211 (p0) cc_final: 0.6541 (p0) REVERT: G 455 TYR cc_start: 0.7849 (m-80) cc_final: 0.6603 (m-80) REVERT: G 461 ARG cc_start: 0.8756 (mpp-170) cc_final: 0.8324 (ptt180) REVERT: G 518 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7348 (m90) REVERT: G 553 ASP cc_start: 0.7481 (t70) cc_final: 0.7266 (t70) REVERT: F 515 TYR cc_start: 0.8557 (m-80) cc_final: 0.8096 (m-10) REVERT: F 546 ARG cc_start: 0.8883 (mpp80) cc_final: 0.8186 (mmt180) REVERT: F 550 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7526 (mtt180) outliers start: 109 outliers final: 81 residues processed: 452 average time/residue: 0.1522 time to fit residues: 107.4080 Evaluate side-chains 428 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 340 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 414 CYS Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 474 CYS Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 518 HIS Chi-restraints excluded: chain J residue 386 ASN Chi-restraints excluded: chain J residue 390 VAL Chi-restraints excluded: chain J residue 428 VAL Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 472 ILE Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 HIS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain H residue 353 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 419 ASN Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 567 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 220 optimal weight: 4.9990 chunk 48 optimal weight: 0.0470 chunk 265 optimal weight: 20.0000 chunk 154 optimal weight: 0.3980 chunk 204 optimal weight: 0.0570 chunk 88 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.141867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.105153 restraints weight = 59937.084| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 4.56 r_work: 0.3765 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23128 Z= 0.134 Angle : 0.744 16.260 31649 Z= 0.370 Chirality : 0.048 0.225 3683 Planarity : 0.005 0.055 4056 Dihedral : 5.870 44.733 3156 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 4.17 % Allowed : 22.24 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.15), residues: 2860 helix: -2.36 (0.29), residues: 213 sheet: -1.03 (0.16), residues: 1044 loop : -1.77 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 416 TYR 0.033 0.002 TYR L 455 PHE 0.016 0.001 PHE C 237 TRP 0.035 0.002 TRP F 488 HIS 0.015 0.001 HIS G 518 Details of bonding type rmsd covalent geometry : bond 0.00308 (23090) covalent geometry : angle 0.73963 (31571) SS BOND : bond 0.00530 ( 36) SS BOND : angle 1.68951 ( 72) hydrogen bonds : bond 0.03955 ( 557) hydrogen bonds : angle 7.08118 ( 1341) link_BETA1-4 : bond 0.00575 ( 1) link_BETA1-4 : angle 2.49024 ( 3) link_NAG-ASN : bond 0.00623 ( 1) link_NAG-ASN : angle 2.21635 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 373 time to evaluate : 0.837 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: C 23 TYR cc_start: 0.7703 (m-80) cc_final: 0.7154 (m-80) REVERT: C 147 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8850 (tp) REVERT: C 176 ASP cc_start: 0.8180 (m-30) cc_final: 0.7536 (t0) REVERT: C 326 LEU cc_start: 0.8502 (tp) cc_final: 0.8191 (tp) REVERT: C 366 TRP cc_start: 0.7941 (t-100) cc_final: 0.7458 (t-100) REVERT: C 382 ASP cc_start: 0.7901 (p0) cc_final: 0.7533 (p0) REVERT: C 398 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7786 (pp) REVERT: C 412 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8380 (pt0) REVERT: C 511 LEU cc_start: 0.6683 (pp) cc_final: 0.6271 (tp) REVERT: A 375 TYR cc_start: 0.7673 (m-10) cc_final: 0.7230 (m-10) REVERT: A 376 ASP cc_start: 0.7779 (m-30) cc_final: 0.7352 (t70) REVERT: A 525 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: B 388 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: B 410 GLU cc_start: 0.6947 (pp20) cc_final: 0.6381 (pp20) REVERT: B 487 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: B 490 GLN cc_start: 0.8356 (pp30) cc_final: 0.7859 (pp30) REVERT: K 487 GLN cc_start: 0.7951 (pt0) cc_final: 0.7708 (pt0) REVERT: L 495 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7699 (mm) REVERT: L 543 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7487 (mt) REVERT: I 375 TYR cc_start: 0.7927 (t80) cc_final: 0.7635 (t80) REVERT: I 414 CYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6521 (p) REVERT: I 416 ASP cc_start: 0.8701 (p0) cc_final: 0.8166 (p0) REVERT: I 453 ASP cc_start: 0.9027 (p0) cc_final: 0.8339 (p0) REVERT: I 489 MET cc_start: 0.7688 (tpp) cc_final: 0.7418 (tpp) REVERT: I 508 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6899 (tm-30) REVERT: J 489 MET cc_start: 0.6947 (mpp) cc_final: 0.5882 (mpp) REVERT: J 525 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: E 346 ARG cc_start: 0.7892 (mmp80) cc_final: 0.6967 (ttt90) REVERT: E 451 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.7391 (mmt-90) REVERT: E 453 ASP cc_start: 0.8245 (t0) cc_final: 0.7663 (t0) REVERT: E 568 MET cc_start: 0.7353 (pmm) cc_final: 0.7027 (pmm) REVERT: H 364 LYS cc_start: 0.6479 (tptt) cc_final: 0.6269 (tptt) REVERT: H 488 TRP cc_start: 0.8320 (m100) cc_final: 0.7552 (m100) REVERT: H 508 GLU cc_start: 0.8043 (tp30) cc_final: 0.7614 (tp30) REVERT: H 534 TYR cc_start: 0.8584 (m-10) cc_final: 0.7862 (m-10) REVERT: G 453 ASP cc_start: 0.8430 (p0) cc_final: 0.7773 (p0) REVERT: G 461 ARG cc_start: 0.8781 (mpp-170) cc_final: 0.8395 (ptt180) REVERT: G 553 ASP cc_start: 0.7471 (t70) cc_final: 0.7018 (t70) REVERT: F 515 TYR cc_start: 0.8590 (m-80) cc_final: 0.8140 (m-10) REVERT: F 546 ARG cc_start: 0.8905 (mpp80) cc_final: 0.8251 (mmt180) REVERT: F 550 ARG cc_start: 0.8276 (ttm110) cc_final: 0.7718 (mtt180) outliers start: 107 outliers final: 78 residues processed: 446 average time/residue: 0.1458 time to fit residues: 102.1053 Evaluate side-chains 438 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 351 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 495 LEU Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 414 CYS Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 474 CYS Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 518 HIS Chi-restraints excluded: chain J residue 390 VAL Chi-restraints excluded: chain J residue 428 VAL Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 472 ILE Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 475 LEU Chi-restraints excluded: chain J residue 518 HIS Chi-restraints excluded: chain J residue 525 GLU Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain H residue 353 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 419 ASN Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 567 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 158 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 80 optimal weight: 0.0050 chunk 119 optimal weight: 9.9990 chunk 195 optimal weight: 0.0670 chunk 67 optimal weight: 4.9990 chunk 182 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 204 optimal weight: 4.9990 overall best weight: 0.7136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.142722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.106479 restraints weight = 59536.604| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 4.57 r_work: 0.3781 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23128 Z= 0.131 Angle : 0.749 16.105 31649 Z= 0.371 Chirality : 0.048 0.295 3683 Planarity : 0.005 0.056 4056 Dihedral : 5.754 44.269 3156 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 4.13 % Allowed : 22.79 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.15), residues: 2860 helix: -2.43 (0.28), residues: 221 sheet: -1.00 (0.16), residues: 1045 loop : -1.68 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 491 TYR 0.034 0.001 TYR L 455 PHE 0.021 0.001 PHE B 424 TRP 0.032 0.002 TRP G 488 HIS 0.019 0.001 HIS E 540 Details of bonding type rmsd covalent geometry : bond 0.00300 (23090) covalent geometry : angle 0.74614 (31571) SS BOND : bond 0.00530 ( 36) SS BOND : angle 1.44745 ( 72) hydrogen bonds : bond 0.03860 ( 557) hydrogen bonds : angle 6.89816 ( 1341) link_BETA1-4 : bond 0.00369 ( 1) link_BETA1-4 : angle 2.52525 ( 3) link_NAG-ASN : bond 0.00781 ( 1) link_NAG-ASN : angle 2.30171 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 387 time to evaluate : 0.744 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: C 23 TYR cc_start: 0.7663 (m-80) cc_final: 0.7118 (m-80) REVERT: C 147 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8840 (tp) REVERT: C 176 ASP cc_start: 0.8144 (m-30) cc_final: 0.7499 (t0) REVERT: C 326 LEU cc_start: 0.8458 (tp) cc_final: 0.8161 (tp) REVERT: C 366 TRP cc_start: 0.7924 (t-100) cc_final: 0.7643 (t-100) REVERT: C 382 ASP cc_start: 0.7875 (p0) cc_final: 0.7487 (p0) REVERT: C 398 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7744 (pp) REVERT: C 412 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8352 (pt0) REVERT: C 511 LEU cc_start: 0.6768 (pp) cc_final: 0.6344 (tp) REVERT: A 375 TYR cc_start: 0.7654 (m-10) cc_final: 0.7233 (m-10) REVERT: A 376 ASP cc_start: 0.7621 (m-30) cc_final: 0.7276 (t70) REVERT: A 525 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: A 553 ASP cc_start: 0.8126 (t0) cc_final: 0.7357 (t70) REVERT: B 388 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: B 410 GLU cc_start: 0.6916 (pp20) cc_final: 0.6312 (pp20) REVERT: B 489 MET cc_start: 0.7758 (tpp) cc_final: 0.7462 (tpp) REVERT: B 490 GLN cc_start: 0.8226 (pp30) cc_final: 0.7790 (pp30) REVERT: B 545 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7379 (t0) REVERT: K 487 GLN cc_start: 0.7970 (pt0) cc_final: 0.7734 (pt0) REVERT: L 400 HIS cc_start: 0.6691 (m170) cc_final: 0.6444 (m170) REVERT: L 487 GLN cc_start: 0.8252 (pt0) cc_final: 0.8018 (pt0) REVERT: L 489 MET cc_start: 0.7494 (mmp) cc_final: 0.6987 (mmm) REVERT: L 495 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7706 (mm) REVERT: L 543 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7459 (mt) REVERT: I 375 TYR cc_start: 0.7894 (t80) cc_final: 0.7609 (t80) REVERT: I 414 CYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6329 (p) REVERT: I 416 ASP cc_start: 0.8668 (p0) cc_final: 0.8121 (p0) REVERT: I 453 ASP cc_start: 0.9038 (p0) cc_final: 0.8422 (p0) REVERT: I 489 MET cc_start: 0.7921 (tpp) cc_final: 0.7571 (tpp) REVERT: J 489 MET cc_start: 0.6791 (mpp) cc_final: 0.5869 (mpp) REVERT: J 525 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: E 346 ARG cc_start: 0.7910 (mmp80) cc_final: 0.6980 (ttt90) REVERT: E 451 ARG cc_start: 0.7689 (mmt-90) cc_final: 0.7240 (mmt-90) REVERT: E 453 ASP cc_start: 0.8203 (t0) cc_final: 0.7618 (t0) REVERT: E 487 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: E 506 MET cc_start: 0.8864 (mpp) cc_final: 0.8616 (mpp) REVERT: E 543 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7862 (mt) REVERT: E 568 MET cc_start: 0.7311 (pmm) cc_final: 0.7107 (pmm) REVERT: H 364 LYS cc_start: 0.6635 (tptt) cc_final: 0.6383 (tptt) REVERT: H 483 ASP cc_start: 0.7601 (t0) cc_final: 0.7337 (t0) REVERT: H 488 TRP cc_start: 0.8412 (m100) cc_final: 0.7794 (m100) REVERT: H 506 MET cc_start: 0.8434 (mpp) cc_final: 0.8020 (mpp) REVERT: H 508 GLU cc_start: 0.8137 (tp30) cc_final: 0.7727 (tp30) REVERT: H 534 TYR cc_start: 0.8580 (m-10) cc_final: 0.7830 (m-10) REVERT: G 453 ASP cc_start: 0.8312 (p0) cc_final: 0.8003 (m-30) REVERT: G 461 ARG cc_start: 0.8783 (mpp-170) cc_final: 0.8411 (ptt180) REVERT: G 489 MET cc_start: 0.7992 (mmm) cc_final: 0.7728 (mmm) REVERT: G 491 ARG cc_start: 0.8315 (mmm160) cc_final: 0.7931 (mmt90) REVERT: G 553 ASP cc_start: 0.7411 (t70) cc_final: 0.6919 (t70) REVERT: F 515 TYR cc_start: 0.8529 (m-80) cc_final: 0.8109 (m-10) REVERT: F 546 ARG cc_start: 0.8911 (mpp80) cc_final: 0.8250 (mmt180) REVERT: F 550 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7771 (mtt180) outliers start: 106 outliers final: 79 residues processed: 462 average time/residue: 0.1517 time to fit residues: 109.1102 Evaluate side-chains 440 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 350 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 495 LEU Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 414 CYS Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 518 HIS Chi-restraints excluded: chain J residue 390 VAL Chi-restraints excluded: chain J residue 428 VAL Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 472 ILE Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 475 LEU Chi-restraints excluded: chain J residue 525 GLU Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 487 GLN Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain H residue 353 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 549 GLU Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 174 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 273 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN B 545 ASN ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.142402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.106254 restraints weight = 60081.267| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 4.51 r_work: 0.3767 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23128 Z= 0.142 Angle : 0.759 14.669 31649 Z= 0.378 Chirality : 0.048 0.230 3683 Planarity : 0.005 0.070 4056 Dihedral : 5.732 44.807 3156 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.86 % Allowed : 23.49 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.15), residues: 2860 helix: -2.40 (0.28), residues: 221 sheet: -0.97 (0.16), residues: 1046 loop : -1.64 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 491 TYR 0.029 0.002 TYR J 534 PHE 0.018 0.001 PHE I 358 TRP 0.030 0.002 TRP E 488 HIS 0.013 0.001 HIS G 518 Details of bonding type rmsd covalent geometry : bond 0.00329 (23090) covalent geometry : angle 0.75618 (31571) SS BOND : bond 0.00571 ( 36) SS BOND : angle 1.42329 ( 72) hydrogen bonds : bond 0.03858 ( 557) hydrogen bonds : angle 6.81816 ( 1341) link_BETA1-4 : bond 0.00793 ( 1) link_BETA1-4 : angle 2.36694 ( 3) link_NAG-ASN : bond 0.00682 ( 1) link_NAG-ASN : angle 2.36908 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 376 time to evaluate : 0.894 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: C 23 TYR cc_start: 0.7685 (m-80) cc_final: 0.7160 (m-80) REVERT: C 147 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8758 (tp) REVERT: C 176 ASP cc_start: 0.8137 (m-30) cc_final: 0.7491 (t0) REVERT: C 326 LEU cc_start: 0.8472 (tp) cc_final: 0.8174 (tp) REVERT: C 366 TRP cc_start: 0.7981 (t-100) cc_final: 0.6872 (t-100) REVERT: C 382 ASP cc_start: 0.7882 (p0) cc_final: 0.7517 (p0) REVERT: C 398 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7769 (pp) REVERT: C 412 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8329 (pt0) REVERT: C 470 PHE cc_start: 0.9042 (m-80) cc_final: 0.7939 (m-80) REVERT: C 511 LEU cc_start: 0.6855 (pp) cc_final: 0.6433 (tp) REVERT: A 375 TYR cc_start: 0.7724 (m-10) cc_final: 0.7287 (m-10) REVERT: A 376 ASP cc_start: 0.7609 (m-30) cc_final: 0.7285 (t70) REVERT: A 525 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: A 553 ASP cc_start: 0.8135 (t0) cc_final: 0.7296 (t70) REVERT: B 388 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: B 410 GLU cc_start: 0.6946 (pp20) cc_final: 0.6350 (pp20) REVERT: B 487 GLN cc_start: 0.7761 (pt0) cc_final: 0.7400 (pm20) REVERT: B 490 GLN cc_start: 0.8323 (pp30) cc_final: 0.7884 (pp30) REVERT: B 545 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7452 (t0) REVERT: L 489 MET cc_start: 0.7586 (mmp) cc_final: 0.7277 (mmp) REVERT: L 495 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7623 (mm) REVERT: L 543 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7560 (mt) REVERT: I 375 TYR cc_start: 0.7864 (t80) cc_final: 0.7601 (t80) REVERT: I 414 CYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6406 (p) REVERT: I 416 ASP cc_start: 0.8665 (p0) cc_final: 0.8126 (p0) REVERT: I 453 ASP cc_start: 0.9023 (p0) cc_final: 0.8422 (p0) REVERT: I 489 MET cc_start: 0.8025 (tpp) cc_final: 0.7672 (tpp) REVERT: I 508 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6530 (tm-30) REVERT: J 489 MET cc_start: 0.6802 (mpp) cc_final: 0.5996 (mpp) REVERT: E 346 ARG cc_start: 0.7914 (mmp80) cc_final: 0.7014 (ttt90) REVERT: E 451 ARG cc_start: 0.7688 (mmt-90) cc_final: 0.7250 (mmt-90) REVERT: E 453 ASP cc_start: 0.8248 (t0) cc_final: 0.7656 (t0) REVERT: E 506 MET cc_start: 0.8831 (mpp) cc_final: 0.8590 (mpp) REVERT: E 543 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7857 (mt) REVERT: E 568 MET cc_start: 0.7377 (pmm) cc_final: 0.7067 (pmm) REVERT: H 364 LYS cc_start: 0.6651 (tptt) cc_final: 0.6395 (tptt) REVERT: H 483 ASP cc_start: 0.7698 (t0) cc_final: 0.7443 (t0) REVERT: H 488 TRP cc_start: 0.8426 (m100) cc_final: 0.7758 (m100) REVERT: H 506 MET cc_start: 0.8459 (mpp) cc_final: 0.8083 (mpp) REVERT: H 508 GLU cc_start: 0.8066 (tp30) cc_final: 0.7701 (tp30) REVERT: H 534 TYR cc_start: 0.8580 (m-10) cc_final: 0.7824 (m-10) REVERT: G 453 ASP cc_start: 0.8271 (p0) cc_final: 0.8018 (m-30) REVERT: G 461 ARG cc_start: 0.8836 (mpp-170) cc_final: 0.8488 (ptt180) REVERT: G 553 ASP cc_start: 0.7403 (t70) cc_final: 0.6902 (t70) REVERT: F 515 TYR cc_start: 0.8573 (m-80) cc_final: 0.8137 (m-10) REVERT: F 546 ARG cc_start: 0.8916 (mpp80) cc_final: 0.8251 (mmt180) REVERT: F 550 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7748 (mtt180) outliers start: 99 outliers final: 79 residues processed: 445 average time/residue: 0.1482 time to fit residues: 103.3120 Evaluate side-chains 445 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 357 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 495 LEU Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 414 CYS Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 518 HIS Chi-restraints excluded: chain J residue 390 VAL Chi-restraints excluded: chain J residue 428 VAL Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 472 ILE Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 475 LEU Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain H residue 353 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 549 GLU Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 547 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 209 optimal weight: 50.0000 chunk 109 optimal weight: 0.6980 chunk 177 optimal weight: 0.4980 chunk 222 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 195 optimal weight: 0.1980 chunk 217 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 HIS B 545 ASN K 487 GLN ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.142866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.106649 restraints weight = 60033.003| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 4.57 r_work: 0.3780 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23128 Z= 0.136 Angle : 0.765 14.094 31649 Z= 0.379 Chirality : 0.047 0.231 3683 Planarity : 0.005 0.073 4056 Dihedral : 5.667 44.525 3156 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 3.66 % Allowed : 23.80 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.16), residues: 2860 helix: -2.39 (0.29), residues: 216 sheet: -0.93 (0.16), residues: 1045 loop : -1.61 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 467 TYR 0.029 0.002 TYR K 534 PHE 0.019 0.001 PHE B 424 TRP 0.032 0.002 TRP G 488 HIS 0.018 0.001 HIS G 518 Details of bonding type rmsd covalent geometry : bond 0.00314 (23090) covalent geometry : angle 0.76294 (31571) SS BOND : bond 0.00539 ( 36) SS BOND : angle 1.34678 ( 72) hydrogen bonds : bond 0.03806 ( 557) hydrogen bonds : angle 6.71533 ( 1341) link_BETA1-4 : bond 0.00597 ( 1) link_BETA1-4 : angle 2.40025 ( 3) link_NAG-ASN : bond 0.00755 ( 1) link_NAG-ASN : angle 2.31709 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 371 time to evaluate : 0.864 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: C 147 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8758 (tp) REVERT: C 176 ASP cc_start: 0.8154 (m-30) cc_final: 0.7530 (t0) REVERT: C 326 LEU cc_start: 0.8490 (tp) cc_final: 0.8155 (tp) REVERT: C 366 TRP cc_start: 0.7960 (t-100) cc_final: 0.6920 (t-100) REVERT: C 382 ASP cc_start: 0.7852 (p0) cc_final: 0.7481 (p0) REVERT: C 398 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7780 (pp) REVERT: C 412 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8364 (pt0) REVERT: C 470 PHE cc_start: 0.9043 (m-80) cc_final: 0.7935 (m-80) REVERT: C 511 LEU cc_start: 0.6857 (pp) cc_final: 0.6422 (tp) REVERT: A 375 TYR cc_start: 0.7757 (m-10) cc_final: 0.7323 (m-10) REVERT: A 376 ASP cc_start: 0.7477 (m-30) cc_final: 0.7207 (t70) REVERT: A 525 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: A 553 ASP cc_start: 0.8180 (t0) cc_final: 0.7309 (t70) REVERT: B 388 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: B 410 GLU cc_start: 0.6935 (pp20) cc_final: 0.6337 (pp20) REVERT: B 489 MET cc_start: 0.7917 (tpp) cc_final: 0.7449 (tpp) REVERT: B 490 GLN cc_start: 0.8242 (pp30) cc_final: 0.7718 (pp30) REVERT: L 489 MET cc_start: 0.7507 (mmp) cc_final: 0.7157 (mmm) REVERT: L 495 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7627 (mm) REVERT: L 543 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7510 (mt) REVERT: I 375 TYR cc_start: 0.7848 (t80) cc_final: 0.7586 (t80) REVERT: I 414 CYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6312 (p) REVERT: I 416 ASP cc_start: 0.8655 (p0) cc_final: 0.8107 (p0) REVERT: I 453 ASP cc_start: 0.9017 (p0) cc_final: 0.8427 (p0) REVERT: I 489 MET cc_start: 0.8078 (tpp) cc_final: 0.7752 (tpp) REVERT: I 508 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6506 (tm-30) REVERT: J 489 MET cc_start: 0.6400 (mpp) cc_final: 0.5785 (mpp) REVERT: J 525 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: E 346 ARG cc_start: 0.7924 (mmp80) cc_final: 0.7018 (ttt90) REVERT: E 451 ARG cc_start: 0.7666 (mmt-90) cc_final: 0.7249 (mmt-90) REVERT: E 453 ASP cc_start: 0.8273 (t0) cc_final: 0.7693 (t0) REVERT: E 506 MET cc_start: 0.8835 (mpp) cc_final: 0.8591 (mpp) REVERT: E 543 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7740 (mt) REVERT: E 568 MET cc_start: 0.7395 (pmm) cc_final: 0.7083 (pmm) REVERT: H 364 LYS cc_start: 0.6649 (tptt) cc_final: 0.6390 (tptt) REVERT: H 483 ASP cc_start: 0.7715 (t0) cc_final: 0.7462 (t0) REVERT: H 488 TRP cc_start: 0.8380 (m100) cc_final: 0.7742 (m100) REVERT: H 506 MET cc_start: 0.8396 (mpp) cc_final: 0.8124 (mpp) REVERT: H 508 GLU cc_start: 0.8123 (tp30) cc_final: 0.7747 (tp30) REVERT: H 534 TYR cc_start: 0.8619 (m-10) cc_final: 0.7868 (m-10) REVERT: G 461 ARG cc_start: 0.8793 (mpp-170) cc_final: 0.8524 (ptt180) REVERT: G 553 ASP cc_start: 0.7339 (t70) cc_final: 0.6865 (t70) REVERT: F 515 TYR cc_start: 0.8540 (m-80) cc_final: 0.8129 (m-10) REVERT: F 546 ARG cc_start: 0.8915 (mpp80) cc_final: 0.8261 (mmt180) REVERT: F 550 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7857 (mtt180) outliers start: 94 outliers final: 80 residues processed: 434 average time/residue: 0.1460 time to fit residues: 100.0596 Evaluate side-chains 448 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 359 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 523 VAL Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 495 LEU Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 566 LEU Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 414 CYS Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 476 VAL Chi-restraints excluded: chain I residue 477 THR Chi-restraints excluded: chain I residue 518 HIS Chi-restraints excluded: chain J residue 390 VAL Chi-restraints excluded: chain J residue 428 VAL Chi-restraints excluded: chain J residue 464 LEU Chi-restraints excluded: chain J residue 472 ILE Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 475 LEU Chi-restraints excluded: chain J residue 522 THR Chi-restraints excluded: chain J residue 525 GLU Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain H residue 353 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 574 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 547 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 29 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 271 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.141643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.105164 restraints weight = 59473.770| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 4.53 r_work: 0.3813 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23128 Z= 0.153 Angle : 0.763 12.969 31649 Z= 0.380 Chirality : 0.048 0.236 3683 Planarity : 0.006 0.079 4056 Dihedral : 5.682 45.191 3156 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.70 % Allowed : 24.07 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.15), residues: 2860 helix: -2.44 (0.29), residues: 210 sheet: -0.93 (0.16), residues: 1027 loop : -1.62 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 491 TYR 0.035 0.002 TYR L 455 PHE 0.016 0.001 PHE E 358 TRP 0.034 0.002 TRP E 488 HIS 0.015 0.001 HIS G 518 Details of bonding type rmsd covalent geometry : bond 0.00355 (23090) covalent geometry : angle 0.76032 (31571) SS BOND : bond 0.00537 ( 36) SS BOND : angle 1.35328 ( 72) hydrogen bonds : bond 0.03807 ( 557) hydrogen bonds : angle 6.68258 ( 1341) link_BETA1-4 : bond 0.00635 ( 1) link_BETA1-4 : angle 2.39571 ( 3) link_NAG-ASN : bond 0.00705 ( 1) link_NAG-ASN : angle 2.56257 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8661.50 seconds wall clock time: 148 minutes 4.63 seconds (8884.63 seconds total)