Starting phenix.real_space_refine on Sun Sep 29 15:16:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/09_2024/7k0c_22591.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/09_2024/7k0c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/09_2024/7k0c_22591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/09_2024/7k0c_22591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/09_2024/7k0c_22591.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0c_22591/09_2024/7k0c_22591.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 15.44, per 1000 atoms: 0.69 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: 5.34 Conformation dependent library (CDL) restraints added in 3.1 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: 3.19 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: 7.76 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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: 7.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.910 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 52.430 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.430 ------------------------------------------------------------------------------- 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 23090 Z= 0.498 Angle : 1.014 14.781 31571 Z= 0.543 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 : 33.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.072 0.003 TRP G 488 HIS 0.009 0.002 HIS H 400 PHE 0.029 0.003 PHE C 237 TYR 0.043 0.003 TYR H 534 ARG 0.023 0.001 ARG G 384 *********************** 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 fitting. rotamer outliers: 3 poor density : 426 time to evaluate : 2.808 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 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 549 GLU cc_start: 0.8349 (pp20) cc_final: 0.7858 (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: 0.7886 (pm20) REVERT: K 487 GLN cc_start: 0.7565 (pp30) cc_final: 0.7285 (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: 0.8227 (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: 0.6481 (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: 0.6573 (m-80) REVERT: H 489 MET cc_start: 0.8709 (mmp) cc_final: 0.8459 (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: 0.6216 (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) outliers start: 3 outliers final: 0 residues processed: 428 average time/residue: 0.3795 time to fit residues: 240.8747 Evaluate side-chains 309 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN C 426 ASN ** 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** B 487 GLN ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** E 540 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23090 Z= 0.285 Angle : 0.836 17.352 31571 Z= 0.429 Chirality : 0.051 0.221 3683 Planarity : 0.006 0.091 4056 Dihedral : 7.048 52.835 3156 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 1.64 % Allowed : 12.31 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.15), residues: 2860 helix: -3.02 (0.26), residues: 210 sheet: -1.61 (0.15), residues: 1098 loop : -2.26 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 488 HIS 0.007 0.001 HIS H 400 PHE 0.022 0.002 PHE B 424 TYR 0.024 0.002 TYR H 455 ARG 0.007 0.001 ARG K 491 *********************** 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 448 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 406 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 TYR cc_start: 0.7339 (m-80) cc_final: 0.6256 (m-80) REVERT: C 49 LEU cc_start: 0.8958 (mm) cc_final: 0.8698 (mm) REVERT: C 176 ASP cc_start: 0.7988 (m-30) cc_final: 0.7389 (t0) REVERT: C 326 LEU cc_start: 0.8432 (tp) cc_final: 0.8061 (tp) REVERT: C 366 TRP cc_start: 0.7808 (t-100) cc_final: 0.6497 (t60) REVERT: C 382 ASP cc_start: 0.7907 (p0) cc_final: 0.7472 (p0) REVERT: C 470 PHE cc_start: 0.9062 (m-80) cc_final: 0.7976 (m-80) REVERT: C 511 LEU cc_start: 0.6625 (pp) cc_final: 0.6057 (tp) REVERT: A 549 GLU cc_start: 0.8111 (pp20) cc_final: 0.7586 (tm-30) REVERT: B 410 GLU cc_start: 0.6835 (pp20) cc_final: 0.6503 (pp20) REVERT: B 423 ARG cc_start: 0.8644 (tmm160) cc_final: 0.7068 (mtm-85) REVERT: B 490 GLN cc_start: 0.8456 (pp30) cc_final: 0.7900 (pp30) REVERT: B 506 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7536 (mtm) REVERT: B 525 GLU cc_start: 0.7898 (pp20) cc_final: 0.7413 (pm20) REVERT: K 483 ASP cc_start: 0.8358 (t0) cc_final: 0.8153 (t0) REVERT: L 418 TRP cc_start: 0.6376 (t-100) cc_final: 0.5683 (t-100) REVERT: L 455 TYR cc_start: 0.6344 (m-80) cc_final: 0.6109 (m-80) REVERT: I 414 CYS cc_start: 0.6843 (p) cc_final: 0.6434 (p) REVERT: I 416 ASP cc_start: 0.8640 (p0) cc_final: 0.8174 (p0) REVERT: I 453 ASP cc_start: 0.8859 (p0) cc_final: 0.8126 (p0) REVERT: I 500 TYR cc_start: 0.6179 (p90) cc_final: 0.5944 (p90) REVERT: J 534 TYR cc_start: 0.8418 (m-10) cc_final: 0.8189 (m-10) REVERT: E 346 ARG cc_start: 0.7324 (mmp80) cc_final: 0.6632 (ttt-90) REVERT: E 453 ASP cc_start: 0.8209 (t0) cc_final: 0.7598 (t0) REVERT: E 455 TYR cc_start: 0.6674 (m-80) cc_final: 0.5869 (m-80) REVERT: E 568 MET cc_start: 0.6463 (pmm) cc_final: 0.5966 (pmm) REVERT: H 364 LYS cc_start: 0.6271 (tptt) cc_final: 0.5947 (tptt) REVERT: H 489 MET cc_start: 0.8539 (mmp) cc_final: 0.8332 (tpp) REVERT: H 526 GLU cc_start: 0.8345 (mp0) cc_final: 0.7893 (pm20) REVERT: H 534 TYR cc_start: 0.8541 (m-80) cc_final: 0.7808 (m-10) REVERT: G 453 ASP cc_start: 0.8306 (p0) cc_final: 0.7765 (p0) REVERT: G 456 LEU cc_start: 0.7661 (tp) cc_final: 0.6902 (tp) REVERT: G 499 LYS cc_start: 0.9023 (mppt) cc_final: 0.8701 (mtmm) REVERT: G 553 ASP cc_start: 0.7512 (t70) cc_final: 0.7093 (t70) REVERT: F 515 TYR cc_start: 0.8552 (m-80) cc_final: 0.8101 (m-10) outliers start: 42 outliers final: 29 residues processed: 427 average time/residue: 0.3564 time to fit residues: 231.2724 Evaluate side-chains 364 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 334 time to evaluate : 2.687 ------------------------------------------------------------------------------- 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 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 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 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 122 THR Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 556 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 215 optimal weight: 40.0000 chunk 176 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 230 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 GLN ** 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 ** 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** H 465 ASN ** 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23090 Z= 0.291 Angle : 0.788 17.215 31571 Z= 0.401 Chirality : 0.049 0.213 3683 Planarity : 0.006 0.071 4056 Dihedral : 6.729 48.191 3156 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.31 % Allowed : 16.83 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.15), residues: 2860 helix: -2.76 (0.28), residues: 200 sheet: -1.44 (0.15), residues: 1066 loop : -2.10 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 488 HIS 0.010 0.001 HIS H 400 PHE 0.014 0.002 PHE A 354 TYR 0.023 0.002 TYR K 375 ARG 0.005 0.001 ARG C 394 *********************** 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 463 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 378 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 TYR cc_start: 0.7380 (m-80) cc_final: 0.6363 (m-80) REVERT: C 49 LEU cc_start: 0.8972 (mm) cc_final: 0.8620 (mm) REVERT: C 176 ASP cc_start: 0.7981 (m-30) cc_final: 0.7382 (t0) REVERT: C 326 LEU cc_start: 0.8487 (tp) cc_final: 0.8157 (tp) REVERT: C 366 TRP cc_start: 0.7871 (t-100) cc_final: 0.6375 (t-100) REVERT: C 382 ASP cc_start: 0.8019 (p0) cc_final: 0.7663 (p0) REVERT: C 398 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7633 (pp) REVERT: C 470 PHE cc_start: 0.9006 (m-80) cc_final: 0.7963 (m-80) REVERT: C 476 TYR cc_start: 0.6878 (p90) cc_final: 0.6601 (p90) REVERT: C 511 LEU cc_start: 0.6689 (pp) cc_final: 0.6102 (tp) REVERT: A 376 ASP cc_start: 0.7880 (m-30) cc_final: 0.7267 (t70) REVERT: B 410 GLU cc_start: 0.6864 (pp20) cc_final: 0.6483 (pp20) REVERT: B 423 ARG cc_start: 0.8616 (tmm160) cc_final: 0.6901 (mtm-85) REVERT: B 490 GLN cc_start: 0.8544 (pp30) cc_final: 0.7879 (pp30) REVERT: B 506 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7486 (mtm) REVERT: B 525 GLU cc_start: 0.7993 (pp20) cc_final: 0.7572 (pm20) REVERT: K 483 ASP cc_start: 0.8413 (t0) cc_final: 0.8209 (t0) REVERT: L 487 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: L 488 TRP cc_start: 0.7519 (m-10) cc_final: 0.7158 (m-10) REVERT: L 489 MET cc_start: 0.7172 (mmp) cc_final: 0.6706 (mmm) REVERT: L 506 MET cc_start: 0.8475 (mmm) cc_final: 0.8217 (mmm) REVERT: I 375 TYR cc_start: 0.8258 (t80) cc_final: 0.7903 (t80) REVERT: I 414 CYS cc_start: 0.6572 (p) cc_final: 0.6171 (p) REVERT: I 416 ASP cc_start: 0.8655 (p0) cc_final: 0.8075 (p0) REVERT: I 439 GLN cc_start: 0.6162 (mt0) cc_final: 0.5938 (mt0) REVERT: I 453 ASP cc_start: 0.8817 (p0) cc_final: 0.8045 (p0) REVERT: I 500 TYR cc_start: 0.6240 (p90) cc_final: 0.5970 (p90) REVERT: E 346 ARG cc_start: 0.7351 (mmp80) cc_final: 0.6634 (ttt-90) REVERT: E 451 ARG cc_start: 0.7802 (mmt-90) cc_final: 0.7430 (mmt-90) REVERT: E 453 ASP cc_start: 0.8122 (t0) cc_final: 0.7433 (t0) REVERT: E 455 TYR cc_start: 0.6639 (m-80) cc_final: 0.5771 (m-80) REVERT: E 533 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8795 (m) REVERT: H 364 LYS cc_start: 0.6335 (tptt) cc_final: 0.6097 (tppt) REVERT: H 508 GLU cc_start: 0.7673 (tp30) cc_final: 0.7385 (tp30) REVERT: H 534 TYR cc_start: 0.8549 (m-10) cc_final: 0.7806 (m-10) REVERT: G 453 ASP cc_start: 0.8435 (p0) cc_final: 0.8011 (p0) REVERT: G 487 GLN cc_start: 0.7224 (tp-100) cc_final: 0.7013 (tp-100) REVERT: G 489 MET cc_start: 0.8223 (mmm) cc_final: 0.7912 (tmm) REVERT: G 491 ARG cc_start: 0.7617 (mmt90) cc_final: 0.7347 (mmm-85) REVERT: G 499 LYS cc_start: 0.9011 (mppt) cc_final: 0.8726 (mtmm) REVERT: G 553 ASP cc_start: 0.7496 (t70) cc_final: 0.7105 (t70) REVERT: F 506 MET cc_start: 0.8935 (mpp) cc_final: 0.8724 (mpp) REVERT: F 515 TYR cc_start: 0.8640 (m-80) cc_final: 0.8118 (m-10) outliers start: 85 outliers final: 54 residues processed: 431 average time/residue: 0.3398 time to fit residues: 224.4966 Evaluate side-chains 407 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 349 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 409 ILE Chi-restraints excluded: chain C residue 437 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 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 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 475 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 487 GLN Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU 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 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 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 477 THR Chi-restraints excluded: chain G residue 488 TRP Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 246 optimal weight: 20.0000 chunk 74 optimal weight: 0.1980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN 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 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 30 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23090 Z= 0.280 Angle : 0.749 17.515 31571 Z= 0.380 Chirality : 0.048 0.227 3683 Planarity : 0.005 0.061 4056 Dihedral : 6.446 47.567 3156 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 4.32 % Allowed : 18.54 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.15), residues: 2860 helix: -2.58 (0.29), residues: 206 sheet: -1.40 (0.15), residues: 1069 loop : -2.03 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 488 HIS 0.007 0.001 HIS H 400 PHE 0.026 0.002 PHE B 424 TYR 0.028 0.002 TYR J 534 ARG 0.006 0.001 ARG C 394 *********************** 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 481 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 370 time to evaluate : 2.832 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: 0.7402 (m-80) cc_final: 0.6441 (m-80) REVERT: C 49 LEU cc_start: 0.8965 (mm) cc_final: 0.8609 (mm) REVERT: C 176 ASP cc_start: 0.7950 (m-30) cc_final: 0.7303 (t0) REVERT: C 326 LEU cc_start: 0.8501 (tp) cc_final: 0.8158 (tp) REVERT: C 366 TRP cc_start: 0.7861 (t-100) cc_final: 0.6354 (t-100) REVERT: C 382 ASP cc_start: 0.8040 (p0) cc_final: 0.7727 (p0) REVERT: C 398 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7607 (pp) REVERT: C 470 PHE cc_start: 0.9010 (m-80) cc_final: 0.7883 (m-80) REVERT: C 476 TYR cc_start: 0.6857 (p90) cc_final: 0.6576 (p90) REVERT: C 511 LEU cc_start: 0.6709 (pp) cc_final: 0.6032 (tp) REVERT: A 376 ASP cc_start: 0.7845 (m-30) cc_final: 0.7310 (t70) REVERT: B 410 GLU cc_start: 0.6926 (pp20) cc_final: 0.6453 (pp20) REVERT: B 423 ARG cc_start: 0.8576 (tmm160) cc_final: 0.6934 (mtm-85) REVERT: B 489 MET cc_start: 0.7649 (tpp) cc_final: 0.7338 (tpp) REVERT: B 490 GLN cc_start: 0.8538 (pp30) cc_final: 0.7847 (pp30) REVERT: B 506 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7493 (mtm) REVERT: B 525 GLU cc_start: 0.8131 (pp20) cc_final: 0.7731 (pm20) REVERT: K 483 ASP cc_start: 0.8469 (t0) cc_final: 0.8265 (t0) REVERT: K 485 PHE cc_start: 0.7554 (t80) cc_final: 0.7210 (t80) REVERT: K 487 GLN cc_start: 0.7582 (pt0) cc_final: 0.7375 (pt0) REVERT: L 391 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8760 (tptp) REVERT: L 475 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8481 (tp) REVERT: I 375 TYR cc_start: 0.8201 (t80) cc_final: 0.7875 (t80) REVERT: I 414 CYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6481 (p) REVERT: I 416 ASP cc_start: 0.8667 (p0) cc_final: 0.8037 (p0) REVERT: I 453 ASP cc_start: 0.8837 (p0) cc_final: 0.8063 (p0) REVERT: I 489 MET cc_start: 0.7918 (tpp) cc_final: 0.7566 (tpp) REVERT: I 500 TYR cc_start: 0.6215 (p90) cc_final: 0.5994 (p90) REVERT: J 488 TRP cc_start: 0.7970 (m-10) cc_final: 0.7458 (m-10) REVERT: J 489 MET cc_start: 0.6750 (mpp) cc_final: 0.5694 (mpp) REVERT: J 491 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7813 (mpp80) REVERT: E 346 ARG cc_start: 0.7391 (mmp80) cc_final: 0.6628 (ttt180) REVERT: E 451 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7323 (mmt-90) REVERT: E 453 ASP cc_start: 0.8091 (t0) cc_final: 0.7355 (t0) REVERT: E 455 TYR cc_start: 0.6629 (m-80) cc_final: 0.5753 (m-80) REVERT: E 489 MET cc_start: 0.7354 (tpp) cc_final: 0.7153 (tpp) REVERT: E 533 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8773 (m) REVERT: H 364 LYS cc_start: 0.6601 (tptt) cc_final: 0.6352 (tppt) REVERT: H 483 ASP cc_start: 0.7496 (t0) cc_final: 0.7218 (t0) REVERT: H 506 MET cc_start: 0.8226 (mpp) cc_final: 0.7941 (mpp) REVERT: H 508 GLU cc_start: 0.7710 (tp30) cc_final: 0.7406 (tp30) REVERT: H 534 TYR cc_start: 0.8550 (m-10) cc_final: 0.7776 (m-10) REVERT: G 453 ASP cc_start: 0.8350 (p0) cc_final: 0.7711 (p0) REVERT: G 487 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.7026 (tp-100) REVERT: G 491 ARG cc_start: 0.7670 (mmt90) cc_final: 0.7340 (mmm-85) REVERT: G 499 LYS cc_start: 0.8998 (mppt) cc_final: 0.8752 (mtmm) REVERT: G 518 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.6668 (m90) REVERT: G 548 THR cc_start: 0.7466 (m) cc_final: 0.7218 (m) REVERT: G 553 ASP cc_start: 0.7486 (t70) cc_final: 0.7075 (t70) REVERT: F 417 ASP cc_start: 0.8553 (m-30) cc_final: 0.8316 (m-30) REVERT: F 515 TYR cc_start: 0.8700 (m-80) cc_final: 0.8184 (m-10) outliers start: 111 outliers final: 68 residues processed: 446 average time/residue: 0.3390 time to fit residues: 232.4499 Evaluate side-chains 413 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 337 time to evaluate : 2.584 ------------------------------------------------------------------------------- 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 368 LEU 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 437 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 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 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 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 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 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 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 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 464 LEU 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 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 396 ILE Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 58 ARG 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 487 GLN Chi-restraints excluded: chain G residue 488 TRP Chi-restraints excluded: chain G residue 518 HIS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 190 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 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 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** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 400 HIS ** 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** F 385 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 23090 Z= 0.318 Angle : 0.768 16.535 31571 Z= 0.389 Chirality : 0.049 0.252 3683 Planarity : 0.006 0.055 4056 Dihedral : 6.419 48.287 3156 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 4.75 % Allowed : 19.59 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.15), residues: 2860 helix: -2.55 (0.29), residues: 206 sheet: -1.45 (0.15), residues: 1078 loop : -1.95 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 488 HIS 0.017 0.001 HIS G 518 PHE 0.018 0.002 PHE G 358 TYR 0.021 0.002 TYR C 36 ARG 0.006 0.001 ARG G 467 *********************** 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 477 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 355 time to evaluate : 3.162 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: C 23 TYR cc_start: 0.7541 (m-80) cc_final: 0.6679 (m-80) REVERT: C 176 ASP cc_start: 0.7987 (m-30) cc_final: 0.7392 (t0) REVERT: C 326 LEU cc_start: 0.8494 (tp) cc_final: 0.8126 (tp) REVERT: C 382 ASP cc_start: 0.8041 (p0) cc_final: 0.7756 (p0) REVERT: C 398 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7608 (pp) REVERT: C 414 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8731 (p) REVERT: C 470 PHE cc_start: 0.9041 (m-80) cc_final: 0.7940 (m-80) REVERT: C 476 TYR cc_start: 0.6824 (p90) cc_final: 0.6610 (p90) REVERT: C 511 LEU cc_start: 0.6782 (pp) cc_final: 0.6098 (tp) REVERT: A 376 ASP cc_start: 0.7990 (m-30) cc_final: 0.7355 (t70) REVERT: B 410 GLU cc_start: 0.6992 (pp20) cc_final: 0.6447 (pp20) REVERT: B 423 ARG cc_start: 0.8559 (tmm160) cc_final: 0.6867 (mtm-85) REVERT: B 487 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8097 (pt0) REVERT: B 490 GLN cc_start: 0.8479 (pp30) cc_final: 0.7811 (pp30) REVERT: B 506 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7400 (mtm) REVERT: B 525 GLU cc_start: 0.8159 (pp20) cc_final: 0.7670 (pm20) REVERT: K 483 ASP cc_start: 0.8495 (t0) cc_final: 0.8291 (t0) REVERT: K 487 GLN cc_start: 0.7650 (pt0) cc_final: 0.7312 (pt0) REVERT: L 475 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8464 (tp) REVERT: L 489 MET cc_start: 0.6720 (mmp) cc_final: 0.6295 (mmm) REVERT: I 375 TYR cc_start: 0.8139 (t80) cc_final: 0.7829 (t80) REVERT: I 414 CYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6213 (p) REVERT: I 416 ASP cc_start: 0.8673 (p0) cc_final: 0.8039 (p0) REVERT: I 453 ASP cc_start: 0.8819 (p0) cc_final: 0.8042 (p0) REVERT: I 489 MET cc_start: 0.7709 (tpp) cc_final: 0.7412 (tpp) REVERT: J 489 MET cc_start: 0.6689 (mpp) cc_final: 0.5666 (mpp) REVERT: J 491 ARG cc_start: 0.8368 (mtt90) cc_final: 0.7846 (mpp80) REVERT: J 534 TYR cc_start: 0.8170 (m-80) cc_final: 0.7943 (m-10) REVERT: E 451 ARG cc_start: 0.7828 (mmt-90) cc_final: 0.7366 (mmt-90) REVERT: E 453 ASP cc_start: 0.8090 (t0) cc_final: 0.7341 (t0) REVERT: E 455 TYR cc_start: 0.6591 (m-80) cc_final: 0.5736 (m-80) REVERT: E 533 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8793 (m) REVERT: H 364 LYS cc_start: 0.6716 (tptt) cc_final: 0.6407 (tptt) REVERT: H 483 ASP cc_start: 0.7454 (t0) cc_final: 0.7191 (t0) REVERT: H 508 GLU cc_start: 0.7732 (tp30) cc_final: 0.7432 (tp30) REVERT: H 534 TYR cc_start: 0.8556 (m-10) cc_final: 0.7766 (m-10) REVERT: G 453 ASP cc_start: 0.8357 (p0) cc_final: 0.7698 (p0) REVERT: G 489 MET cc_start: 0.8335 (mmm) cc_final: 0.7843 (tmm) REVERT: G 491 ARG cc_start: 0.7739 (mmt90) cc_final: 0.7475 (mmm-85) REVERT: G 499 LYS cc_start: 0.8995 (mppt) cc_final: 0.8767 (mtmm) REVERT: G 518 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.7667 (m90) REVERT: G 553 ASP cc_start: 0.7375 (t70) cc_final: 0.6939 (t70) REVERT: F 515 TYR cc_start: 0.8739 (m-80) cc_final: 0.8214 (m-10) outliers start: 122 outliers final: 86 residues processed: 441 average time/residue: 0.3340 time to fit residues: 229.6465 Evaluate side-chains 431 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 337 time to evaluate : 3.215 ------------------------------------------------------------------------------- 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 368 LEU 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 414 THR Chi-restraints excluded: chain C residue 437 ILE 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 A residue 564 VAL Chi-restraints excluded: chain B residue 359 LEU 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 473 THR Chi-restraints excluded: chain B residue 475 LEU 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 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 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 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 474 CYS Chi-restraints excluded: chain I residue 475 LEU 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 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 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 464 LEU 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 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 H residue 561 LEU 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 417 ASP Chi-restraints excluded: chain G residue 419 ASN Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 488 TRP Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain F residue 413 ILE 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 92 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 chunk 228 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 144 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 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 465 ASN G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23090 Z= 0.242 Angle : 0.740 17.023 31571 Z= 0.373 Chirality : 0.048 0.226 3683 Planarity : 0.005 0.054 4056 Dihedral : 6.172 46.138 3156 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 4.36 % Allowed : 20.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.15), residues: 2860 helix: -2.35 (0.30), residues: 202 sheet: -1.30 (0.15), residues: 1070 loop : -1.84 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 488 HIS 0.022 0.001 HIS G 518 PHE 0.027 0.001 PHE B 424 TYR 0.036 0.002 TYR L 455 ARG 0.006 0.001 ARG G 467 *********************** 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 482 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 370 time to evaluate : 2.628 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: 0.7466 (m-80) cc_final: 0.6673 (m-80) REVERT: C 176 ASP cc_start: 0.7969 (m-30) cc_final: 0.7381 (t0) REVERT: C 326 LEU cc_start: 0.8463 (tp) cc_final: 0.8093 (tp) REVERT: C 382 ASP cc_start: 0.7893 (p0) cc_final: 0.7559 (p0) REVERT: C 398 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7606 (pp) REVERT: C 412 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8398 (pt0) REVERT: C 414 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8810 (p) REVERT: C 470 PHE cc_start: 0.9001 (m-80) cc_final: 0.7866 (m-80) REVERT: C 511 LEU cc_start: 0.6420 (pp) cc_final: 0.6092 (tp) REVERT: A 376 ASP cc_start: 0.7777 (m-30) cc_final: 0.7257 (t70) REVERT: B 410 GLU cc_start: 0.7097 (pp20) cc_final: 0.6572 (pp20) REVERT: B 487 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: B 490 GLN cc_start: 0.8518 (pp30) cc_final: 0.7860 (pp30) REVERT: B 506 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7391 (mtm) REVERT: B 545 ASN cc_start: 0.7862 (t0) cc_final: 0.7661 (t0) REVERT: L 391 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8680 (tptp) REVERT: L 475 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8339 (tp) REVERT: L 548 THR cc_start: 0.7884 (m) cc_final: 0.7656 (m) REVERT: I 375 TYR cc_start: 0.8037 (t80) cc_final: 0.7729 (t80) REVERT: I 414 CYS cc_start: 0.6518 (OUTLIER) cc_final: 0.6250 (p) REVERT: I 416 ASP cc_start: 0.8659 (p0) cc_final: 0.8029 (p0) REVERT: I 453 ASP cc_start: 0.8823 (p0) cc_final: 0.8020 (p0) REVERT: I 487 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7381 (tm-30) REVERT: I 489 MET cc_start: 0.7681 (tpp) cc_final: 0.7296 (tpp) REVERT: J 451 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7506 (tpp80) REVERT: J 489 MET cc_start: 0.6858 (mpp) cc_final: 0.5811 (mpp) REVERT: J 491 ARG cc_start: 0.8474 (mtt90) cc_final: 0.8056 (mpp80) REVERT: J 514 ARG cc_start: 0.7918 (mmt90) cc_final: 0.7581 (mmt90) REVERT: E 346 ARG cc_start: 0.7450 (mmp80) cc_final: 0.6596 (ttt90) REVERT: E 451 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7304 (mmt-90) REVERT: E 453 ASP cc_start: 0.8039 (t0) cc_final: 0.7376 (t0) REVERT: E 533 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8752 (m) REVERT: E 568 MET cc_start: 0.7176 (pmm) cc_final: 0.6844 (pmm) REVERT: H 364 LYS cc_start: 0.6513 (tptt) cc_final: 0.6212 (tptt) REVERT: H 483 ASP cc_start: 0.7618 (t0) cc_final: 0.7354 (t0) REVERT: H 506 MET cc_start: 0.8458 (mpp) cc_final: 0.8223 (mpp) REVERT: H 534 TYR cc_start: 0.8546 (m-10) cc_final: 0.7752 (m-10) REVERT: G 453 ASP cc_start: 0.8216 (p0) cc_final: 0.7514 (p0) REVERT: G 491 ARG cc_start: 0.7603 (mmt90) cc_final: 0.7316 (mmm-85) REVERT: G 518 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7421 (m90) REVERT: G 553 ASP cc_start: 0.7644 (t70) cc_final: 0.7352 (t70) REVERT: F 515 TYR cc_start: 0.8713 (m-80) cc_final: 0.8214 (m-10) REVERT: F 546 ARG cc_start: 0.8854 (mpp80) cc_final: 0.8153 (mmt180) outliers start: 112 outliers final: 78 residues processed: 443 average time/residue: 0.3330 time to fit residues: 228.8306 Evaluate side-chains 435 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 348 time to evaluate : 2.631 ------------------------------------------------------------------------------- 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 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 414 THR Chi-restraints excluded: chain C residue 437 ILE 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 538 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain B residue 359 LEU 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 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 472 ILE Chi-restraints excluded: chain L residue 475 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 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 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 522 THR Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 549 GLU 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 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 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 475 LEU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 488 TRP Chi-restraints excluded: chain G residue 518 HIS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 157 optimal weight: 0.0980 chunk 201 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 153 optimal weight: 0.5980 chunk 274 optimal weight: 1.9990 chunk 171 optimal weight: 30.0000 chunk 167 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23090 Z= 0.332 Angle : 0.770 15.347 31571 Z= 0.389 Chirality : 0.049 0.229 3683 Planarity : 0.005 0.055 4056 Dihedral : 6.256 47.442 3156 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 4.95 % Allowed : 21.11 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.15), residues: 2860 helix: -2.47 (0.29), residues: 207 sheet: -1.28 (0.15), residues: 1076 loop : -1.87 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 488 HIS 0.013 0.001 HIS G 518 PHE 0.015 0.002 PHE K 358 TYR 0.051 0.002 TYR L 455 ARG 0.006 0.001 ARG G 467 *********************** 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 471 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 344 time to evaluate : 2.637 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 49 LEU cc_start: 0.9006 (mm) cc_final: 0.8674 (mt) REVERT: C 147 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8818 (tp) REVERT: C 176 ASP cc_start: 0.8172 (m-30) cc_final: 0.7534 (t0) REVERT: C 177 ILE cc_start: 0.6270 (OUTLIER) cc_final: 0.6026 (mp) REVERT: C 326 LEU cc_start: 0.8503 (tp) cc_final: 0.8124 (tp) REVERT: C 382 ASP cc_start: 0.7956 (p0) cc_final: 0.7698 (p0) REVERT: C 398 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7643 (pp) REVERT: C 414 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8945 (p) REVERT: C 470 PHE cc_start: 0.9009 (m-80) cc_final: 0.7937 (m-80) REVERT: C 476 TYR cc_start: 0.6491 (p90) cc_final: 0.6240 (p90) REVERT: C 511 LEU cc_start: 0.6437 (pp) cc_final: 0.6111 (tp) REVERT: A 376 ASP cc_start: 0.7815 (m-30) cc_final: 0.7261 (t70) REVERT: A 530 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8779 (p) REVERT: B 410 GLU cc_start: 0.6877 (pp20) cc_final: 0.6335 (pp20) REVERT: B 487 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: B 490 GLN cc_start: 0.8556 (pp30) cc_final: 0.7955 (pp30) REVERT: B 506 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7342 (mtm) REVERT: K 415 GLU cc_start: 0.9013 (mp0) cc_final: 0.8671 (mm-30) REVERT: L 495 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7794 (mm) REVERT: I 375 TYR cc_start: 0.7935 (t80) cc_final: 0.7679 (t80) REVERT: I 414 CYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6234 (p) REVERT: I 416 ASP cc_start: 0.8675 (p0) cc_final: 0.8040 (p0) REVERT: I 453 ASP cc_start: 0.8831 (p0) cc_final: 0.8011 (p0) REVERT: I 489 MET cc_start: 0.7966 (tpp) cc_final: 0.7569 (tpp) REVERT: J 489 MET cc_start: 0.6947 (mpp) cc_final: 0.5882 (mpp) REVERT: J 491 ARG cc_start: 0.8540 (mtt90) cc_final: 0.8108 (mpp80) REVERT: J 534 TYR cc_start: 0.8124 (m-80) cc_final: 0.7814 (m-80) REVERT: E 346 ARG cc_start: 0.7508 (mmp80) cc_final: 0.6624 (ttt90) REVERT: E 451 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7300 (mmt-90) REVERT: E 453 ASP cc_start: 0.8049 (t0) cc_final: 0.7363 (t0) REVERT: E 533 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8779 (m) REVERT: H 364 LYS cc_start: 0.6660 (tptt) cc_final: 0.6376 (tptt) REVERT: H 483 ASP cc_start: 0.7523 (t0) cc_final: 0.7260 (t0) REVERT: H 508 GLU cc_start: 0.7799 (tp30) cc_final: 0.7505 (tp30) REVERT: H 534 TYR cc_start: 0.8557 (m-10) cc_final: 0.7758 (m-10) REVERT: D 32 ASP cc_start: 0.7664 (t0) cc_final: 0.7424 (t0) REVERT: G 453 ASP cc_start: 0.8394 (p0) cc_final: 0.7695 (p0) REVERT: G 489 MET cc_start: 0.8079 (mmm) cc_final: 0.7835 (tmm) REVERT: G 491 ARG cc_start: 0.7704 (mmt90) cc_final: 0.7462 (mmt90) REVERT: G 518 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7549 (m90) REVERT: G 553 ASP cc_start: 0.7609 (t70) cc_final: 0.7309 (t70) REVERT: F 515 TYR cc_start: 0.8746 (m-80) cc_final: 0.8224 (m-10) outliers start: 127 outliers final: 97 residues processed: 437 average time/residue: 0.3136 time to fit residues: 215.0381 Evaluate side-chains 439 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 330 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 177 ILE 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 409 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 437 ILE 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 380 ILE 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 A residue 554 LYS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 359 LEU 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 506 MET 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 538 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 473 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 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 477 THR Chi-restraints excluded: chain I residue 518 HIS Chi-restraints excluded: chain I residue 566 LEU 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 475 LEU Chi-restraints excluded: chain J residue 522 THR 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 441 ILE Chi-restraints excluded: chain E residue 451 ARG 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 473 THR Chi-restraints excluded: chain H residue 484 VAL 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 417 ASP 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 488 TRP Chi-restraints excluded: chain G residue 502 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 40.0000 chunk 109 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 174 optimal weight: 0.5980 chunk 187 optimal weight: 30.0000 chunk 135 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 249 optimal weight: 20.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23090 Z= 0.344 Angle : 0.793 15.731 31571 Z= 0.400 Chirality : 0.049 0.371 3683 Planarity : 0.006 0.056 4056 Dihedral : 6.310 47.829 3156 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 5.10 % Allowed : 21.93 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2860 helix: -2.51 (0.29), residues: 207 sheet: -1.32 (0.15), residues: 1082 loop : -1.87 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 488 HIS 0.020 0.001 HIS E 540 PHE 0.025 0.002 PHE B 424 TYR 0.048 0.002 TYR L 455 ARG 0.008 0.001 ARG C 394 *********************** 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 474 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 343 time to evaluate : 2.260 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 49 LEU cc_start: 0.9032 (mm) cc_final: 0.8695 (mt) REVERT: C 147 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8833 (tp) REVERT: C 176 ASP cc_start: 0.8189 (m-30) cc_final: 0.7542 (t0) REVERT: C 177 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5983 (mp) REVERT: C 326 LEU cc_start: 0.8506 (tp) cc_final: 0.8113 (tp) REVERT: C 382 ASP cc_start: 0.7975 (p0) cc_final: 0.7729 (p0) REVERT: C 398 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7637 (pp) REVERT: C 414 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8794 (p) REVERT: C 470 PHE cc_start: 0.9015 (m-80) cc_final: 0.7927 (m-80) REVERT: C 511 LEU cc_start: 0.6448 (pp) cc_final: 0.6120 (tp) REVERT: A 375 TYR cc_start: 0.7607 (m-10) cc_final: 0.7089 (m-10) REVERT: A 376 ASP cc_start: 0.7855 (m-30) cc_final: 0.7323 (t70) REVERT: A 530 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8781 (p) REVERT: B 410 GLU cc_start: 0.6960 (pp20) cc_final: 0.6445 (pp20) REVERT: B 487 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: B 490 GLN cc_start: 0.8568 (pp30) cc_final: 0.7999 (pp30) REVERT: B 506 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7362 (mtm) REVERT: L 475 LEU cc_start: 0.8551 (tt) cc_final: 0.8349 (tp) REVERT: L 489 MET cc_start: 0.7357 (mmp) cc_final: 0.6780 (mmm) REVERT: L 495 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7797 (mm) REVERT: L 548 THR cc_start: 0.7769 (m) cc_final: 0.7515 (m) REVERT: I 375 TYR cc_start: 0.7968 (t80) cc_final: 0.7696 (t80) REVERT: I 414 CYS cc_start: 0.6645 (OUTLIER) cc_final: 0.6235 (p) REVERT: I 416 ASP cc_start: 0.8678 (p0) cc_final: 0.8064 (p0) REVERT: I 453 ASP cc_start: 0.8738 (p0) cc_final: 0.7911 (p0) REVERT: I 489 MET cc_start: 0.8081 (tpp) cc_final: 0.7696 (tpp) REVERT: J 488 TRP cc_start: 0.7989 (m-10) cc_final: 0.7460 (m-10) REVERT: J 489 MET cc_start: 0.7084 (mpp) cc_final: 0.5916 (mpp) REVERT: J 514 ARG cc_start: 0.8011 (mmt90) cc_final: 0.7641 (mmt90) REVERT: J 525 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: J 534 TYR cc_start: 0.8242 (m-80) cc_final: 0.7836 (m-10) REVERT: E 451 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7328 (mmt-90) REVERT: E 453 ASP cc_start: 0.8027 (t0) cc_final: 0.7334 (t0) REVERT: E 533 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8782 (m) REVERT: E 568 MET cc_start: 0.7152 (pmm) cc_final: 0.6792 (pmm) REVERT: H 364 LYS cc_start: 0.6630 (tptt) cc_final: 0.6337 (tptt) REVERT: H 508 GLU cc_start: 0.7763 (tp30) cc_final: 0.7464 (tp30) REVERT: H 534 TYR cc_start: 0.8555 (m-10) cc_final: 0.7755 (m-10) REVERT: D 32 ASP cc_start: 0.7610 (t0) cc_final: 0.7374 (t0) REVERT: G 453 ASP cc_start: 0.8258 (p0) cc_final: 0.7856 (p0) REVERT: G 489 MET cc_start: 0.8102 (mmm) cc_final: 0.7859 (tmm) REVERT: G 553 ASP cc_start: 0.7597 (t70) cc_final: 0.7313 (t70) REVERT: F 515 TYR cc_start: 0.8749 (m-80) cc_final: 0.8231 (m-10) outliers start: 131 outliers final: 107 residues processed: 437 average time/residue: 0.3265 time to fit residues: 224.2794 Evaluate side-chains 445 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 326 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 177 ILE 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 409 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 437 ILE 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 380 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 508 GLU 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 A residue 554 LYS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 359 LEU 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 506 MET 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 537 VAL Chi-restraints excluded: chain K residue 538 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 473 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 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 477 THR Chi-restraints excluded: chain I residue 518 HIS Chi-restraints excluded: chain I residue 566 LEU 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 475 LEU Chi-restraints excluded: chain J residue 518 HIS 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 441 ILE Chi-restraints excluded: chain E residue 451 ARG 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 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 457 LEU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 518 HIS 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 417 ASP 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 488 TRP Chi-restraints excluded: chain G residue 496 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 255 optimal weight: 0.1980 chunk 154 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 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** G 465 ASN G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23090 Z= 0.244 Angle : 0.769 16.542 31571 Z= 0.384 Chirality : 0.048 0.314 3683 Planarity : 0.005 0.055 4056 Dihedral : 6.098 46.498 3156 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 4.67 % Allowed : 22.71 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.15), residues: 2860 helix: -2.41 (0.29), residues: 207 sheet: -1.21 (0.16), residues: 1068 loop : -1.81 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 488 HIS 0.018 0.001 HIS G 518 PHE 0.011 0.001 PHE C 466 TYR 0.045 0.002 TYR L 455 ARG 0.012 0.001 ARG L 491 *********************** 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 474 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 354 time to evaluate : 2.672 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 147 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8872 (tp) REVERT: C 176 ASP cc_start: 0.8153 (m-30) cc_final: 0.7523 (t0) REVERT: C 177 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5954 (mp) REVERT: C 326 LEU cc_start: 0.8499 (tp) cc_final: 0.8122 (tp) REVERT: C 382 ASP cc_start: 0.7903 (p0) cc_final: 0.7578 (p0) REVERT: C 398 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7628 (pp) REVERT: C 414 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8799 (p) REVERT: C 470 PHE cc_start: 0.9004 (m-80) cc_final: 0.7883 (m-80) REVERT: C 511 LEU cc_start: 0.6613 (pp) cc_final: 0.6265 (tp) REVERT: A 375 TYR cc_start: 0.7526 (m-10) cc_final: 0.7021 (m-10) REVERT: A 376 ASP cc_start: 0.7758 (m-30) cc_final: 0.7289 (t70) REVERT: A 530 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8770 (p) REVERT: B 410 GLU cc_start: 0.6949 (pp20) cc_final: 0.6402 (pp20) REVERT: B 487 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8021 (pt0) REVERT: B 490 GLN cc_start: 0.8461 (pp30) cc_final: 0.7927 (pp30) REVERT: B 506 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7321 (mtm) REVERT: L 489 MET cc_start: 0.7342 (mmp) cc_final: 0.6878 (mmm) REVERT: L 495 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7620 (mm) REVERT: I 375 TYR cc_start: 0.7962 (t80) cc_final: 0.7689 (t80) REVERT: I 414 CYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6317 (p) REVERT: I 416 ASP cc_start: 0.8675 (p0) cc_final: 0.7998 (p0) REVERT: I 453 ASP cc_start: 0.8850 (p0) cc_final: 0.8073 (p0) REVERT: I 489 MET cc_start: 0.8087 (tpp) cc_final: 0.7741 (tpp) REVERT: J 489 MET cc_start: 0.6773 (mpp) cc_final: 0.5851 (mpp) REVERT: J 491 ARG cc_start: 0.8496 (mtt90) cc_final: 0.7964 (mpp80) REVERT: J 525 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: J 534 TYR cc_start: 0.8279 (m-80) cc_final: 0.7777 (m-10) REVERT: E 451 ARG cc_start: 0.7748 (mmt-90) cc_final: 0.7225 (mmt-90) REVERT: E 453 ASP cc_start: 0.7989 (t0) cc_final: 0.7292 (t0) REVERT: E 533 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8750 (m) REVERT: E 568 MET cc_start: 0.7158 (pmm) cc_final: 0.6828 (pmm) REVERT: H 364 LYS cc_start: 0.6478 (tptt) cc_final: 0.6156 (tptt) REVERT: H 506 MET cc_start: 0.8347 (mpp) cc_final: 0.7892 (mpp) REVERT: H 534 TYR cc_start: 0.8523 (m-10) cc_final: 0.7722 (m-10) REVERT: H 548 THR cc_start: 0.7951 (m) cc_final: 0.7741 (m) REVERT: H 568 MET cc_start: 0.7564 (pmm) cc_final: 0.7251 (pmm) REVERT: D 63 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.7058 (m-10) REVERT: D 124 MET cc_start: 0.8785 (tpt) cc_final: 0.8165 (tpt) REVERT: G 453 ASP cc_start: 0.8182 (p0) cc_final: 0.7469 (p0) REVERT: G 548 THR cc_start: 0.7770 (m) cc_final: 0.7481 (m) REVERT: G 553 ASP cc_start: 0.7699 (t70) cc_final: 0.7492 (t70) REVERT: F 515 TYR cc_start: 0.8696 (m-80) cc_final: 0.8209 (m-10) REVERT: F 546 ARG cc_start: 0.8855 (mpp80) cc_final: 0.8175 (mmt180) outliers start: 120 outliers final: 95 residues processed: 440 average time/residue: 0.3195 time to fit residues: 220.6958 Evaluate side-chains 441 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 334 time to evaluate : 2.625 ------------------------------------------------------------------------------- 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 177 ILE 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 409 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 437 ILE 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 508 GLU 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 A residue 554 LYS Chi-restraints excluded: chain B residue 359 LEU 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 487 GLN Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 530 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 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 370 THR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 472 ILE 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 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 477 THR Chi-restraints excluded: chain I residue 518 HIS Chi-restraints excluded: chain I residue 566 LEU 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 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 441 ILE Chi-restraints excluded: chain E residue 447 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 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 457 LEU Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 525 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 63 TYR 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 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 475 LEU Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 488 TRP 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 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 165 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 188 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 174 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 HIS ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 ASN G 518 HIS ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23090 Z= 0.207 Angle : 0.764 17.313 31571 Z= 0.379 Chirality : 0.048 0.291 3683 Planarity : 0.005 0.061 4056 Dihedral : 5.882 45.088 3156 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 3.90 % Allowed : 23.80 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.16), residues: 2860 helix: -2.28 (0.30), residues: 214 sheet: -1.08 (0.16), residues: 1053 loop : -1.77 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 488 HIS 0.022 0.001 HIS G 518 PHE 0.020 0.001 PHE B 424 TYR 0.042 0.002 TYR L 455 ARG 0.009 0.001 ARG F 550 ********************** 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 466 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 366 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 LEU cc_start: 0.9030 (mm) cc_final: 0.8704 (mm) REVERT: C 147 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8844 (tp) REVERT: C 176 ASP cc_start: 0.8042 (m-30) cc_final: 0.7535 (t0) REVERT: C 326 LEU cc_start: 0.8522 (tp) cc_final: 0.8168 (tp) REVERT: C 382 ASP cc_start: 0.7845 (p0) cc_final: 0.7520 (p0) REVERT: C 398 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7549 (pp) REVERT: C 414 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8797 (p) REVERT: C 470 PHE cc_start: 0.8962 (m-80) cc_final: 0.8094 (m-80) REVERT: C 511 LEU cc_start: 0.6639 (pp) cc_final: 0.6222 (tp) REVERT: A 375 TYR cc_start: 0.7538 (m-10) cc_final: 0.7091 (m-10) REVERT: A 376 ASP cc_start: 0.7555 (m-30) cc_final: 0.7193 (t70) REVERT: A 530 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8842 (p) REVERT: B 410 GLU cc_start: 0.6850 (pp20) cc_final: 0.6233 (pp20) REVERT: B 487 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8031 (pt0) REVERT: B 490 GLN cc_start: 0.8452 (pp30) cc_final: 0.7910 (pp30) REVERT: B 506 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7284 (mtm) REVERT: B 530 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8724 (p) REVERT: B 545 ASN cc_start: 0.7507 (t0) cc_final: 0.7280 (t0) REVERT: L 391 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8675 (tptp) REVERT: L 489 MET cc_start: 0.7217 (mmp) cc_final: 0.6793 (mmm) REVERT: L 495 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7639 (mm) REVERT: L 498 GLU cc_start: 0.8484 (mp0) cc_final: 0.8264 (pm20) REVERT: I 375 TYR cc_start: 0.7885 (t80) cc_final: 0.7644 (t80) REVERT: I 414 CYS cc_start: 0.6377 (OUTLIER) cc_final: 0.6015 (p) REVERT: I 416 ASP cc_start: 0.8670 (p0) cc_final: 0.8113 (p0) REVERT: I 453 ASP cc_start: 0.8853 (p0) cc_final: 0.8075 (p0) REVERT: I 489 MET cc_start: 0.8085 (tpp) cc_final: 0.7743 (tpp) REVERT: J 488 TRP cc_start: 0.7905 (m-10) cc_final: 0.7495 (m-10) REVERT: J 489 MET cc_start: 0.6896 (mpp) cc_final: 0.5937 (mpp) REVERT: J 525 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: J 534 TYR cc_start: 0.8273 (m-80) cc_final: 0.7772 (m-10) REVERT: E 451 ARG cc_start: 0.7647 (mmt-90) cc_final: 0.7130 (mmt-90) REVERT: E 453 ASP cc_start: 0.7974 (t0) cc_final: 0.7291 (t0) REVERT: E 487 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: E 533 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8739 (m) REVERT: E 568 MET cc_start: 0.7100 (pmm) cc_final: 0.6784 (pmm) REVERT: H 364 LYS cc_start: 0.6468 (tptt) cc_final: 0.6160 (tptt) REVERT: H 506 MET cc_start: 0.8306 (mpp) cc_final: 0.7872 (mpp) REVERT: H 534 TYR cc_start: 0.8490 (m-10) cc_final: 0.7693 (m-10) REVERT: H 548 THR cc_start: 0.7926 (m) cc_final: 0.7717 (m) REVERT: D 124 MET cc_start: 0.8745 (tpt) cc_final: 0.7952 (tpt) REVERT: G 453 ASP cc_start: 0.7957 (p0) cc_final: 0.7582 (p0) REVERT: G 461 ARG cc_start: 0.8846 (mpp-170) cc_final: 0.8362 (ptt180) REVERT: G 553 ASP cc_start: 0.7516 (t70) cc_final: 0.7076 (t70) REVERT: F 515 TYR cc_start: 0.8668 (m-80) cc_final: 0.8201 (m-10) REVERT: F 546 ARG cc_start: 0.8866 (mpp80) cc_final: 0.8185 (mmt180) outliers start: 100 outliers final: 78 residues processed: 438 average time/residue: 0.3612 time to fit residues: 248.4088 Evaluate side-chains 429 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 339 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 414 THR 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 530 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain B residue 359 LEU 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 487 GLN Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 530 THR 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 538 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 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 472 ILE Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 HIS Chi-restraints excluded: chain J residue 525 GLU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 447 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 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 H residue 518 HIS 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 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 488 TRP Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 536 CYS 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 69 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN C 140 ASN C 530 GLN ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 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 463 GLN ** J 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.136628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.099090 restraints weight = 60844.723| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 4.46 r_work: 0.3640 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 23090 Z= 0.454 Angle : 0.851 13.990 31571 Z= 0.431 Chirality : 0.051 0.284 3683 Planarity : 0.007 0.086 4056 Dihedral : 6.355 48.275 3156 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 4.52 % Allowed : 23.65 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.15), residues: 2860 helix: -2.67 (0.27), residues: 214 sheet: -1.34 (0.15), residues: 1083 loop : -1.85 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP E 488 HIS 0.020 0.002 HIS G 518 PHE 0.028 0.002 PHE I 358 TYR 0.051 0.003 TYR L 455 ARG 0.013 0.001 ARG G 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6387.17 seconds wall clock time: 114 minutes 1.16 seconds (6841.16 seconds total)