Starting phenix.real_space_refine on Fri Mar 6 11:50:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vnj_32041/03_2026/7vnj_32041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnj_32041/03_2026/7vnj_32041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vnj_32041/03_2026/7vnj_32041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnj_32041/03_2026/7vnj_32041.map" model { file = "/net/cci-nas-00/data/ceres_data/7vnj_32041/03_2026/7vnj_32041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnj_32041/03_2026/7vnj_32041.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 47 5.16 5 C 19184 2.51 5 N 4992 2.21 5 O 6417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30661 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "B" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "C" Number of atoms: 3867 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Chain: "D" Number of atoms: 3966 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 3898 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 477} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 496, 3888 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 476} Chain breaks: 2 bond proxies already assigned to first conformer: 3885 Chain: "E" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "F" Number of atoms: 3867 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Chain: "G" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 464} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 3776 Chain: "H" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3200 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 73 residue: pdb=" N AGLY A 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 488 " occ=0.50 residue: pdb=" N ATHR A 489 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 489 " occ=0.50 residue: pdb=" N ALYS A 490 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 490 " occ=0.50 residue: pdb=" N AASN A 491 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 491 " occ=0.50 residue: pdb=" N ASER A 492 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 492 " occ=0.50 residue: pdb=" N ASER A 493 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 493 " occ=0.50 residue: pdb=" N AGLY A 494 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 494 " occ=0.50 residue: pdb=" N AGLN A 495 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 495 " occ=0.50 residue: pdb=" N AILE A 496 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 496 " occ=0.50 residue: pdb=" N AVAL A 497 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 497 " occ=0.50 residue: pdb=" N THR A 498 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 THR A 498 " occ=0.50 residue: pdb=" N AGLY B 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 488 " occ=0.50 ... (remaining 61 not shown) Time building chain proxies: 10.51, per 1000 atoms: 0.34 Number of scatterers: 30661 At special positions: 0 Unit cell: (177.76, 179.52, 187.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 21 19.99 S 47 16.00 O 6417 8.00 N 4992 7.00 C 19184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 2.4 seconds 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7316 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 81 sheets defined 20.2% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.555A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.552A pdb=" N ILE A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.532A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.689A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.946A pdb=" N ASP B 291 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.778A pdb=" N ILE B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.595A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 594 removed outlier: 3.658A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.542A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.780A pdb=" N ILE C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 503 through 513 removed outlier: 4.823A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 594 removed outlier: 3.617A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 251 removed outlier: 3.653A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.654A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.844A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 503 through 513 removed outlier: 4.507A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 556 Processing helix chain 'D' and resid 572 through 576 removed outlier: 3.753A pdb=" N VAL D 576 " --> pdb=" O GLU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 595 removed outlier: 3.592A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 291 removed outlier: 4.078A pdb=" N ASP E 291 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.762A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 503 through 513 removed outlier: 4.519A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE E 513 " --> pdb=" O GLN E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 595 removed outlier: 3.560A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.573A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 291 removed outlier: 3.682A pdb=" N ASP F 291 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.564A pdb=" N ILE F 429 " --> pdb=" O GLU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 503 through 513 removed outlier: 4.723A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE F 513 " --> pdb=" O GLN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 581 through 595 removed outlier: 3.776A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR F 594 " --> pdb=" O ASP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.527A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.662A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.698A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 471 Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.602A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.775A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR G 594 " --> pdb=" O ASP G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing helix chain 'H' and resid 20 through 30 removed outlier: 3.703A pdb=" N LYS H 30 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 60 through 67 removed outlier: 3.731A pdb=" N ILE H 64 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU H 65 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 4.106A pdb=" N ASN H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 115 through 126 Processing helix chain 'H' and resid 216 through 229 Processing helix chain 'H' and resid 231 through 235 Processing helix chain 'H' and resid 236 through 250 Processing helix chain 'H' and resid 250 through 260 removed outlier: 3.553A pdb=" N SER H 260 " --> pdb=" O ASN H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 266 Processing helix chain 'H' and resid 268 through 285 removed outlier: 4.311A pdb=" N LYS H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU H 285 " --> pdb=" O ALA H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 315 through 327 removed outlier: 3.731A pdb=" N ILE H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.629A pdb=" N ALA H 350 " --> pdb=" O SER H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 372 No H-bonds generated for 'chain 'H' and resid 370 through 372' Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 311 removed outlier: 6.795A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 439 removed outlier: 3.915A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 331 removed outlier: 3.514A pdb=" N SER A 316 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL G 367 " --> pdb=" O ASN F 329 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL F 367 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER E 316 " --> pdb=" O GLY E 378 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 316 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 370 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 316 " --> pdb=" O GLY C 378 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 316 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 370 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.869A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN A 432 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.869A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 531 removed outlier: 9.364A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 618 through 620 removed outlier: 4.463A pdb=" N LEU A 736 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER A 672 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 738 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 670 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A 740 " --> pdb=" O ARG A 668 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG A 668 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 675 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 705 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 618 through 620 removed outlier: 4.463A pdb=" N LEU A 736 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER A 672 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 738 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 670 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A 740 " --> pdb=" O ARG A 668 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG A 668 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.564A pdb=" N ILE A 723 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 722 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB5, first strand: chain 'B' and resid 300 through 311 removed outlier: 5.714A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.821A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.934A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN B 432 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.934A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AC1, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.344A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AC3, first strand: chain 'B' and resid 618 through 620 removed outlier: 5.519A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 668 " --> pdb=" O LEU B 741 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 618 through 620 removed outlier: 5.519A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 668 " --> pdb=" O LEU B 741 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 655 through 658 removed outlier: 3.530A pdb=" N LEU B 698 " --> pdb=" O ILE B 684 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC7, first strand: chain 'C' and resid 300 through 311 removed outlier: 5.804A pdb=" N VAL C 302 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR C 396 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 438 through 439 removed outlier: 3.981A pdb=" N ALA C 387 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.943A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR C 404 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN C 432 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.943A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AD3, first strand: chain 'C' and resid 526 through 531 removed outlier: 9.302A pdb=" N ILE C 611 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AD5, first strand: chain 'C' and resid 618 through 620 removed outlier: 5.713A pdb=" N LEU C 733 " --> pdb=" O LYS C 676 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS C 676 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASN C 735 " --> pdb=" O TYR C 674 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR C 674 " --> pdb=" O ASN C 735 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG C 668 " --> pdb=" O LEU C 741 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C 705 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 618 through 620 removed outlier: 5.713A pdb=" N LEU C 733 " --> pdb=" O LYS C 676 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS C 676 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASN C 735 " --> pdb=" O TYR C 674 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR C 674 " --> pdb=" O ASN C 735 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG C 668 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 655 through 658 removed outlier: 3.573A pdb=" N GLU C 722 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AD9, first strand: chain 'D' and resid 300 through 311 removed outlier: 6.815A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 438 through 439 removed outlier: 3.914A pdb=" N ALA D 387 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE D 460 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.903A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR D 404 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN D 432 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.903A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY D 485 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR D 407 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL D 483 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AE5, first strand: chain 'D' and resid 526 through 531 removed outlier: 9.303A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AE7, first strand: chain 'D' and resid 618 through 620 removed outlier: 5.494A pdb=" N LEU D 733 " --> pdb=" O LYS D 676 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LYS D 676 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASN D 735 " --> pdb=" O TYR D 674 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR D 674 " --> pdb=" O ASN D 735 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 655 through 658 removed outlier: 3.847A pdb=" N ILE D 656 " --> pdb=" O ILE D 723 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU D 722 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 689 " --> pdb=" O GLU D 722 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 688 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 694 " --> pdb=" O ILE D 688 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AF1, first strand: chain 'E' and resid 300 through 311 removed outlier: 5.737A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 438 through 439 removed outlier: 3.959A pdb=" N ALA E 387 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.978A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR E 404 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 432 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.978A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS E 405 " --> pdb=" O GLY E 485 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY E 485 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR E 407 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL E 483 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AF6, first strand: chain 'E' and resid 526 through 531 removed outlier: 9.333A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AF8, first strand: chain 'E' and resid 618 through 620 removed outlier: 4.394A pdb=" N LEU E 736 " --> pdb=" O SER E 672 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER E 672 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE E 738 " --> pdb=" O VAL E 670 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL E 670 " --> pdb=" O ILE E 738 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU E 740 " --> pdb=" O ARG E 668 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG E 668 " --> pdb=" O GLU E 740 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 705 " --> pdb=" O SER E 675 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 618 through 620 removed outlier: 4.394A pdb=" N LEU E 736 " --> pdb=" O SER E 672 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER E 672 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE E 738 " --> pdb=" O VAL E 670 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL E 670 " --> pdb=" O ILE E 738 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU E 740 " --> pdb=" O ARG E 668 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG E 668 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 655 through 658 removed outlier: 3.552A pdb=" N ILE E 656 " --> pdb=" O ILE E 723 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 723 " --> pdb=" O ILE E 656 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 722 " --> pdb=" O LYS E 689 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 698 " --> pdb=" O ILE E 684 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS E 694 " --> pdb=" O ILE E 688 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AG3, first strand: chain 'F' and resid 300 through 311 removed outlier: 6.908A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 438 through 439 removed outlier: 3.941A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.849A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR F 404 " --> pdb=" O ASN F 432 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN F 432 " --> pdb=" O TYR F 404 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.849A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AG8, first strand: chain 'F' and resid 524 through 531 removed outlier: 3.778A pdb=" N GLU F 524 " --> pdb=" O THR F 521 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AH1, first strand: chain 'F' and resid 618 through 620 removed outlier: 5.394A pdb=" N LEU F 733 " --> pdb=" O LYS F 676 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS F 676 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN F 735 " --> pdb=" O TYR F 674 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR F 674 " --> pdb=" O ASN F 735 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR F 705 " --> pdb=" O SER F 675 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 618 through 620 removed outlier: 5.394A pdb=" N LEU F 733 " --> pdb=" O LYS F 676 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS F 676 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN F 735 " --> pdb=" O TYR F 674 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR F 674 " --> pdb=" O ASN F 735 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS F 667 " --> pdb=" O THR F 713 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 713 " --> pdb=" O LYS F 667 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 655 through 658 removed outlier: 3.859A pdb=" N ILE F 723 " --> pdb=" O ILE F 656 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP F 696 " --> pdb=" O VAL F 686 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE F 688 " --> pdb=" O LYS F 694 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS F 694 " --> pdb=" O ILE F 688 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AH5, first strand: chain 'G' and resid 300 through 311 removed outlier: 6.814A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 438 through 439 removed outlier: 3.892A pdb=" N ALA G 387 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.834A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR G 404 " --> pdb=" O ASN G 432 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN G 432 " --> pdb=" O TYR G 404 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.834A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS G 405 " --> pdb=" O AGLY G 485 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N AGLY G 485 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR G 407 " --> pdb=" O AVAL G 483 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N AVAL G 483 " --> pdb=" O THR G 407 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR G 409 " --> pdb=" O ATHR G 481 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AI1, first strand: chain 'G' and resid 525 through 531 removed outlier: 9.328A pdb=" N ILE G 611 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 558 through 559 Processing sheet with id=AI3, first strand: chain 'G' and resid 618 through 620 removed outlier: 5.251A pdb=" N LEU G 733 " --> pdb=" O LYS G 676 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS G 676 " --> pdb=" O LEU G 733 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG G 668 " --> pdb=" O LEU G 741 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR G 705 " --> pdb=" O SER G 675 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 618 through 620 removed outlier: 5.251A pdb=" N LEU G 733 " --> pdb=" O LYS G 676 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS G 676 " --> pdb=" O LEU G 733 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG G 668 " --> pdb=" O LEU G 741 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 655 through 658 removed outlier: 3.843A pdb=" N GLU G 722 " --> pdb=" O LYS G 689 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP G 696 " --> pdb=" O VAL G 686 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE G 688 " --> pdb=" O LYS G 694 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS G 694 " --> pdb=" O ILE G 688 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 89 through 94 removed outlier: 4.044A pdb=" N VAL H 207 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS H 198 " --> pdb=" O VAL H 194 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL H 194 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR H 200 " --> pdb=" O ARG H 192 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG H 192 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS H 202 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE H 190 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU H 204 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER H 184 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR H 183 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 136 through 139 removed outlier: 3.811A pdb=" N THR H 177 " --> pdb=" O ILE H 139 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'H' and resid 291 through 297 removed outlier: 4.105A pdb=" N ILE H 354 " --> pdb=" O SER H 297 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL H 355 " --> pdb=" O VAL H 407 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA H 409 " --> pdb=" O VAL H 355 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ARG H 357 " --> pdb=" O ALA H 409 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU H 411 " --> pdb=" O ARG H 357 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR H 359 " --> pdb=" O LEU H 411 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS H 393 " --> pdb=" O ASP H 408 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR H 410 " --> pdb=" O ILE H 391 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE H 391 " --> pdb=" O THR H 410 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE H 412 " --> pdb=" O PHE H 389 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N PHE H 389 " --> pdb=" O ILE H 412 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER H 387 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'H' and resid 337 through 340 removed outlier: 3.975A pdb=" N ILE H 337 " --> pdb=" O LEU H 383 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 2979 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: 8.90 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10048 1.34 - 1.46: 5723 1.46 - 1.58: 15319 1.58 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 31177 Sorted by residual: bond pdb=" N SER C 280 " pdb=" CA SER C 280 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.12e-02 7.97e+03 6.81e+00 bond pdb=" N PHE E 281 " pdb=" CA PHE E 281 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.17e-02 7.31e+03 6.34e+00 bond pdb=" N PHE G 281 " pdb=" CA PHE G 281 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.17e-02 7.31e+03 6.32e+00 bond pdb=" N ASP E 282 " pdb=" CA ASP E 282 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.20e+00 bond pdb=" N PHE B 281 " pdb=" CA PHE B 281 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.17e-02 7.31e+03 6.14e+00 ... (remaining 31172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 41826 2.08 - 4.17: 381 4.17 - 6.25: 37 6.25 - 8.33: 2 8.33 - 10.41: 5 Bond angle restraints: 42251 Sorted by residual: angle pdb=" CA PHE D 281 " pdb=" CB PHE D 281 " pdb=" CG PHE D 281 " ideal model delta sigma weight residual 113.80 119.39 -5.59 1.00e+00 1.00e+00 3.12e+01 angle pdb=" CA PHE F 281 " pdb=" CB PHE F 281 " pdb=" CG PHE F 281 " ideal model delta sigma weight residual 113.80 119.00 -5.20 1.00e+00 1.00e+00 2.71e+01 angle pdb=" CA PHE B 281 " pdb=" CB PHE B 281 " pdb=" CG PHE B 281 " ideal model delta sigma weight residual 113.80 118.91 -5.11 1.00e+00 1.00e+00 2.62e+01 angle pdb=" CA PHE A 281 " pdb=" CB PHE A 281 " pdb=" CG PHE A 281 " ideal model delta sigma weight residual 113.80 118.89 -5.09 1.00e+00 1.00e+00 2.60e+01 angle pdb=" CA PHE G 281 " pdb=" CB PHE G 281 " pdb=" CG PHE G 281 " ideal model delta sigma weight residual 113.80 118.81 -5.01 1.00e+00 1.00e+00 2.51e+01 ... (remaining 42246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 17333 17.98 - 35.96: 1335 35.96 - 53.93: 251 53.93 - 71.91: 56 71.91 - 89.89: 27 Dihedral angle restraints: 19002 sinusoidal: 7571 harmonic: 11431 Sorted by residual: dihedral pdb=" CA ASN F 223 " pdb=" C ASN F 223 " pdb=" N ASP F 224 " pdb=" CA ASP F 224 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA THR B 714 " pdb=" C THR B 714 " pdb=" N GLU B 715 " pdb=" CA GLU B 715 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA PRO E 659 " pdb=" C PRO E 659 " pdb=" N MET E 660 " pdb=" CA MET E 660 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 18999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2816 0.029 - 0.058: 1159 0.058 - 0.086: 362 0.086 - 0.115: 322 0.115 - 0.144: 99 Chirality restraints: 4758 Sorted by residual: chirality pdb=" CA ILE G 569 " pdb=" N ILE G 569 " pdb=" C ILE G 569 " pdb=" CB ILE G 569 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE E 569 " pdb=" N ILE E 569 " pdb=" C ILE E 569 " pdb=" CB ILE E 569 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE B 569 " pdb=" N ILE B 569 " pdb=" C ILE B 569 " pdb=" CB ILE B 569 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 4755 not shown) Planarity restraints: 5493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 664 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO B 665 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 664 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO A 665 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 665 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 665 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 278 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C SER B 278 " -0.039 2.00e-02 2.50e+03 pdb=" O SER B 278 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 279 " 0.013 2.00e-02 2.50e+03 ... (remaining 5490 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1238 2.71 - 3.26: 29146 3.26 - 3.81: 47931 3.81 - 4.35: 64012 4.35 - 4.90: 107366 Nonbonded interactions: 249693 Sorted by model distance: nonbonded pdb=" O PHE H 313 " pdb=" OG1 THR H 403 " model vdw 2.166 3.040 nonbonded pdb=" NH2 ARG D 394 " pdb=" O LEU D 444 " model vdw 2.216 3.120 nonbonded pdb=" NH2 ARG B 394 " pdb=" O LEU B 444 " model vdw 2.234 3.120 nonbonded pdb=" NH2 ARG F 394 " pdb=" O LEU F 444 " model vdw 2.235 3.120 nonbonded pdb=" NH2 ARG C 394 " pdb=" O LEU C 444 " model vdw 2.241 3.120 ... (remaining 249688 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 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'B' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'C' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'D' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'E' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'F' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) selection = (chain 'G' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 903)) } 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=0.50 max=1.00 mean=0.99 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: 7.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.240 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.003 0.051 31177 Z= 0.152 Angle : 0.521 10.414 42251 Z= 0.292 Chirality : 0.044 0.144 4758 Planarity : 0.004 0.071 5493 Dihedral : 13.796 89.890 11686 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.40 % Allowed : 0.52 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3884 helix: 0.65 (0.22), residues: 630 sheet: 0.38 (0.16), residues: 1217 loop : -1.04 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 33 TYR 0.017 0.001 TYR G 704 PHE 0.012 0.001 PHE B 707 TRP 0.015 0.001 TRP D 214 HIS 0.001 0.000 AHIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00317 (31177) covalent geometry : angle 0.52106 (42251) hydrogen bonds : bond 0.21484 ( 1124) hydrogen bonds : angle 8.37699 ( 2979) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 477 time to evaluate : 1.112 Fit side-chains REVERT: A 269 ASP cc_start: 0.8176 (p0) cc_final: 0.7917 (p0) REVERT: A 321 LYS cc_start: 0.5690 (ttpp) cc_final: 0.5303 (mtmt) REVERT: A 376 ASN cc_start: 0.7114 (m-40) cc_final: 0.6515 (t0) REVERT: A 452 MET cc_start: 0.8667 (ptt) cc_final: 0.8465 (ptt) REVERT: B 247 ASP cc_start: 0.7364 (m-30) cc_final: 0.6905 (p0) REVERT: B 269 ASP cc_start: 0.8083 (p0) cc_final: 0.7741 (p0) REVERT: B 313 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 314 HIS cc_start: 0.6637 (m-70) cc_final: 0.6179 (t70) REVERT: B 318 ASP cc_start: 0.6801 (m-30) cc_final: 0.6340 (m-30) REVERT: B 319 GLN cc_start: 0.6854 (tt0) cc_final: 0.6653 (tt0) REVERT: B 426 GLU cc_start: 0.7841 (mm-30) cc_final: 0.6856 (pm20) REVERT: B 582 ASP cc_start: 0.7758 (m-30) cc_final: 0.7087 (m-30) REVERT: B 586 ASN cc_start: 0.7410 (m-40) cc_final: 0.7113 (m110) REVERT: B 711 PHE cc_start: 0.5932 (p90) cc_final: 0.5422 (p90) REVERT: C 248 SER cc_start: 0.7088 (p) cc_final: 0.6713 (t) REVERT: C 269 ASP cc_start: 0.7374 (p0) cc_final: 0.7119 (p0) REVERT: C 313 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6967 (mt-10) REVERT: C 314 HIS cc_start: 0.6838 (m-70) cc_final: 0.6634 (m90) REVERT: C 318 ASP cc_start: 0.6395 (m-30) cc_final: 0.6151 (m-30) REVERT: C 319 GLN cc_start: 0.7030 (pt0) cc_final: 0.6565 (pt0) REVERT: C 382 ASN cc_start: 0.7883 (t0) cc_final: 0.7654 (t160) REVERT: C 544 GLU cc_start: 0.7377 (tt0) cc_final: 0.7102 (tt0) REVERT: C 582 ASP cc_start: 0.7250 (m-30) cc_final: 0.6854 (t0) REVERT: D 290 ARG cc_start: 0.7422 (mtp85) cc_final: 0.7075 (mtp180) REVERT: D 319 GLN cc_start: 0.6631 (pt0) cc_final: 0.6326 (mt0) REVERT: D 382 ASN cc_start: 0.8240 (t0) cc_final: 0.7922 (t0) REVERT: D 523 ASN cc_start: 0.7657 (p0) cc_final: 0.7307 (p0) REVERT: D 598 LYS cc_start: 0.7481 (mmtp) cc_final: 0.7216 (mmtm) REVERT: D 660 MET cc_start: 0.5591 (tpt) cc_final: 0.4930 (tpp) REVERT: E 252 GLN cc_start: 0.7032 (mt0) cc_final: 0.6260 (mm-40) REVERT: E 313 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6394 (mt-10) REVERT: E 319 GLN cc_start: 0.6612 (pt0) cc_final: 0.6369 (mt0) REVERT: E 321 LYS cc_start: 0.6133 (ttpt) cc_final: 0.5572 (tttt) REVERT: E 373 GLU cc_start: 0.6480 (pt0) cc_final: 0.6210 (pt0) REVERT: E 468 LYS cc_start: 0.6977 (mmtt) cc_final: 0.6775 (mmmt) REVERT: E 565 TYR cc_start: 0.7234 (m-80) cc_final: 0.6938 (m-10) REVERT: E 711 PHE cc_start: 0.6301 (p90) cc_final: 0.5945 (p90) REVERT: E 738 ILE cc_start: 0.6871 (mt) cc_final: 0.6485 (mm) REVERT: F 255 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7552 (mptt) REVERT: F 314 HIS cc_start: 0.6074 (m-70) cc_final: 0.5778 (t-90) REVERT: F 321 LYS cc_start: 0.6352 (ttpp) cc_final: 0.5932 (tttm) REVERT: F 373 GLU cc_start: 0.6269 (pt0) cc_final: 0.5372 (pm20) REVERT: F 396 TYR cc_start: 0.7340 (p90) cc_final: 0.7113 (p90) REVERT: F 740 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6197 (mt-10) REVERT: G 319 GLN cc_start: 0.6065 (tt0) cc_final: 0.5840 (tt0) REVERT: G 324 SER cc_start: 0.6542 (t) cc_final: 0.6203 (m) REVERT: G 376 ASN cc_start: 0.6777 (m-40) cc_final: 0.6199 (m-40) REVERT: G 396 TYR cc_start: 0.7788 (p90) cc_final: 0.7521 (p90) REVERT: G 417 ASP cc_start: 0.7547 (m-30) cc_final: 0.7266 (m-30) REVERT: G 522 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6491 (mm-30) REVERT: G 582 ASP cc_start: 0.7145 (m-30) cc_final: 0.6749 (t0) REVERT: H 40 GLU cc_start: 0.5546 (mm-30) cc_final: 0.5267 (tm-30) REVERT: H 58 TYR cc_start: 0.5264 (m-80) cc_final: 0.4956 (m-80) REVERT: H 65 GLU cc_start: 0.4533 (mt-10) cc_final: 0.4063 (tp30) REVERT: H 78 ASN cc_start: 0.4854 (m-40) cc_final: 0.4324 (m-40) REVERT: H 109 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6428 (tm-30) REVERT: H 143 GLU cc_start: 0.6376 (mt-10) cc_final: 0.6056 (mt-10) REVERT: H 156 MET cc_start: 0.7620 (mmm) cc_final: 0.6975 (mmm) REVERT: H 206 SER cc_start: 0.7143 (p) cc_final: 0.6725 (t) REVERT: H 216 ASP cc_start: 0.5272 (m-30) cc_final: 0.5054 (p0) REVERT: H 233 ASN cc_start: 0.4070 (m-40) cc_final: 0.3786 (t0) REVERT: H 311 TYR cc_start: 0.3826 (t80) cc_final: 0.3400 (t80) REVERT: H 317 GLU cc_start: 0.4918 (tp30) cc_final: 0.4563 (mp0) REVERT: H 322 PHE cc_start: 0.5126 (t80) cc_final: 0.4891 (t80) outliers start: 8 outliers final: 9 residues processed: 485 average time/residue: 0.6168 time to fit residues: 355.4608 Evaluate side-chains 261 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 252 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 0.0470 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 634 ASN B 265 ASN B 463 ASN C 265 ASN C 392 ASN C 602 ASN D 371 ASN D 463 ASN D 735 ASN F 392 ASN F 583 ASN G 392 ASN G 536 GLN G 702 GLN H 127 GLN H 385 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.160294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123859 restraints weight = 133158.590| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 5.32 r_work: 0.2914 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.003 0.054 31177 Z= 0.130 Angle : 0.569 15.677 42251 Z= 0.305 Chirality : 0.046 0.184 4758 Planarity : 0.004 0.061 5493 Dihedral : 4.670 42.296 4211 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.79 % Allowed : 6.90 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3884 helix: 1.03 (0.22), residues: 602 sheet: 0.64 (0.15), residues: 1230 loop : -0.86 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 77 TYR 0.032 0.001 TYR H 246 PHE 0.012 0.002 PHE C 711 TRP 0.012 0.001 TRP A 245 HIS 0.004 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00278 (31177) covalent geometry : angle 0.56855 (42251) hydrogen bonds : bond 0.03369 ( 1124) hydrogen bonds : angle 5.17061 ( 2979) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 0.909 Fit side-chains REVERT: A 269 ASP cc_start: 0.8409 (p0) cc_final: 0.8155 (p0) REVERT: A 319 GLN cc_start: 0.7547 (pt0) cc_final: 0.7114 (pt0) REVERT: A 321 LYS cc_start: 0.6626 (ttpp) cc_final: 0.6069 (ttpt) REVERT: A 376 ASN cc_start: 0.7897 (m-40) cc_final: 0.7383 (t0) REVERT: B 313 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8068 (mt-10) REVERT: B 318 ASP cc_start: 0.7410 (m-30) cc_final: 0.7075 (m-30) REVERT: B 426 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8061 (pm20) REVERT: B 582 ASP cc_start: 0.8097 (m-30) cc_final: 0.7615 (m-30) REVERT: C 544 GLU cc_start: 0.8442 (tt0) cc_final: 0.8106 (mt-10) REVERT: C 569 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7947 (mp) REVERT: C 582 ASP cc_start: 0.7964 (m-30) cc_final: 0.7599 (m-30) REVERT: C 589 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7636 (ttmm) REVERT: C 621 ASN cc_start: 0.7010 (p0) cc_final: 0.6807 (p0) REVERT: C 660 MET cc_start: 0.6630 (tpt) cc_final: 0.6285 (mmt) REVERT: D 290 ARG cc_start: 0.8297 (mtp85) cc_final: 0.8082 (mtp180) REVERT: D 318 ASP cc_start: 0.6981 (m-30) cc_final: 0.6700 (m-30) REVERT: D 376 ASN cc_start: 0.7927 (m-40) cc_final: 0.7726 (m-40) REVERT: D 382 ASN cc_start: 0.8651 (t0) cc_final: 0.8341 (t0) REVERT: D 458 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7124 (ttt-90) REVERT: D 660 MET cc_start: 0.5756 (tpt) cc_final: 0.5398 (tmt) REVERT: E 252 GLN cc_start: 0.8177 (mt0) cc_final: 0.7497 (mm110) REVERT: E 290 ARG cc_start: 0.8389 (mtp85) cc_final: 0.8149 (mtp180) REVERT: E 313 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7612 (mt-10) REVERT: E 321 LYS cc_start: 0.7184 (ttpt) cc_final: 0.6577 (tttt) REVERT: E 376 ASN cc_start: 0.7528 (m-40) cc_final: 0.7265 (t0) REVERT: E 707 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.5782 (p90) REVERT: E 711 PHE cc_start: 0.7066 (p90) cc_final: 0.6679 (p90) REVERT: E 738 ILE cc_start: 0.7614 (mt) cc_final: 0.7231 (mp) REVERT: F 255 LYS cc_start: 0.8848 (mmtp) cc_final: 0.8485 (mptt) REVERT: F 314 HIS cc_start: 0.7404 (m-70) cc_final: 0.7079 (t70) REVERT: F 321 LYS cc_start: 0.7100 (ttpp) cc_final: 0.6764 (tttm) REVERT: F 371 ASN cc_start: 0.6762 (OUTLIER) cc_final: 0.6534 (p0) REVERT: F 373 GLU cc_start: 0.6786 (pt0) cc_final: 0.5939 (pm20) REVERT: G 376 ASN cc_start: 0.7460 (m-40) cc_final: 0.7172 (m-40) REVERT: G 417 ASP cc_start: 0.8471 (m-30) cc_final: 0.8179 (m-30) REVERT: G 520 ASP cc_start: 0.8574 (t0) cc_final: 0.8190 (m-30) REVERT: G 522 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7012 (mm-30) REVERT: G 582 ASP cc_start: 0.7759 (m-30) cc_final: 0.7430 (t0) REVERT: H 26 ARG cc_start: 0.4431 (tmm160) cc_final: 0.3827 (ptt90) REVERT: H 40 GLU cc_start: 0.5824 (mm-30) cc_final: 0.5548 (tm-30) REVERT: H 60 TYR cc_start: 0.4270 (m-80) cc_final: 0.4055 (m-80) REVERT: H 65 GLU cc_start: 0.4899 (mt-10) cc_final: 0.4381 (tp30) REVERT: H 77 ARG cc_start: 0.5397 (ttp80) cc_final: 0.5137 (ttp-110) REVERT: H 78 ASN cc_start: 0.5379 (m-40) cc_final: 0.4785 (m-40) REVERT: H 109 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6544 (tm-30) REVERT: H 117 GLU cc_start: 0.6234 (mp0) cc_final: 0.5991 (pm20) REVERT: H 143 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6280 (mt-10) REVERT: H 146 LYS cc_start: 0.5472 (OUTLIER) cc_final: 0.4929 (tptp) REVERT: H 156 MET cc_start: 0.8047 (mmm) cc_final: 0.7781 (mmm) REVERT: H 216 ASP cc_start: 0.5286 (m-30) cc_final: 0.4805 (p0) REVERT: H 233 ASN cc_start: 0.4110 (m-40) cc_final: 0.3803 (t0) REVERT: H 317 GLU cc_start: 0.5159 (tp30) cc_final: 0.4687 (mp0) REVERT: H 369 LEU cc_start: 0.4565 (mt) cc_final: 0.4273 (mt) outliers start: 56 outliers final: 27 residues processed: 329 average time/residue: 0.5912 time to fit residues: 233.1773 Evaluate side-chains 273 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 617 THR Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 387 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 244 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 0.0870 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 735 ASN B 463 ASN B 634 ASN C 225 ASN C 252 GLN D 392 ASN D 735 ASN E 368 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.156241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118073 restraints weight = 149195.720| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 5.39 r_work: 0.2817 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31177 Z= 0.168 Angle : 0.618 17.057 42251 Z= 0.334 Chirality : 0.047 0.198 4758 Planarity : 0.004 0.060 5493 Dihedral : 5.013 41.327 4207 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.19 % Allowed : 9.06 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 3884 helix: 0.96 (0.22), residues: 590 sheet: 0.78 (0.15), residues: 1189 loop : -0.97 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 248 TYR 0.029 0.002 TYR B 704 PHE 0.024 0.002 PHE C 711 TRP 0.011 0.001 TRP A 632 HIS 0.004 0.001 AHIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00390 (31177) covalent geometry : angle 0.61785 (42251) hydrogen bonds : bond 0.04427 ( 1124) hydrogen bonds : angle 5.16988 ( 2979) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 242 time to evaluate : 1.184 Fit side-chains REVERT: A 319 GLN cc_start: 0.7625 (pt0) cc_final: 0.7206 (pt0) REVERT: A 321 LYS cc_start: 0.6549 (ttpp) cc_final: 0.6087 (ttmt) REVERT: A 371 ASN cc_start: 0.6755 (p0) cc_final: 0.6338 (m-40) REVERT: A 376 ASN cc_start: 0.7984 (m-40) cc_final: 0.7426 (t0) REVERT: A 499 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8110 (tp30) REVERT: B 313 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8119 (mt-10) REVERT: B 582 ASP cc_start: 0.8209 (m-30) cc_final: 0.7755 (m-30) REVERT: C 218 ASP cc_start: 0.6520 (p0) cc_final: 0.6096 (m-30) REVERT: C 381 ILE cc_start: 0.8055 (tp) cc_final: 0.7657 (pt) REVERT: C 491 ASN cc_start: 0.6540 (t0) cc_final: 0.6324 (t0) REVERT: C 536 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7475 (mp-120) REVERT: C 544 GLU cc_start: 0.8647 (tt0) cc_final: 0.8364 (mt-10) REVERT: C 569 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8063 (mp) REVERT: C 582 ASP cc_start: 0.7951 (m-30) cc_final: 0.7688 (m-30) REVERT: C 589 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7753 (ptmm) REVERT: C 621 ASN cc_start: 0.6903 (p0) cc_final: 0.6645 (p0) REVERT: D 317 THR cc_start: 0.8151 (m) cc_final: 0.7857 (p) REVERT: D 318 ASP cc_start: 0.7238 (m-30) cc_final: 0.6951 (m-30) REVERT: D 458 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7129 (ttt-90) REVERT: D 660 MET cc_start: 0.6005 (tpt) cc_final: 0.5615 (tmt) REVERT: E 252 GLN cc_start: 0.8107 (mt0) cc_final: 0.7531 (mm110) REVERT: E 321 LYS cc_start: 0.7168 (ttpt) cc_final: 0.6890 (ttmm) REVERT: E 589 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7921 (tttm) REVERT: E 606 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: E 707 PHE cc_start: 0.6495 (OUTLIER) cc_final: 0.4932 (p90) REVERT: E 711 PHE cc_start: 0.6948 (p90) cc_final: 0.6460 (p90) REVERT: E 738 ILE cc_start: 0.7784 (mt) cc_final: 0.7470 (mp) REVERT: F 314 HIS cc_start: 0.7573 (m-70) cc_final: 0.7336 (t70) REVERT: F 373 GLU cc_start: 0.7014 (pt0) cc_final: 0.6104 (pm20) REVERT: G 291 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.7835 (p0) REVERT: G 376 ASN cc_start: 0.7859 (m-40) cc_final: 0.7651 (m-40) REVERT: G 468 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8385 (mmtm) REVERT: G 582 ASP cc_start: 0.7992 (m-30) cc_final: 0.7736 (t0) REVERT: H 26 ARG cc_start: 0.4533 (tmm160) cc_final: 0.3498 (ttm110) REVERT: H 65 GLU cc_start: 0.4847 (mt-10) cc_final: 0.4370 (tp30) REVERT: H 77 ARG cc_start: 0.5741 (ttp80) cc_final: 0.5439 (ttp80) REVERT: H 78 ASN cc_start: 0.5187 (m-40) cc_final: 0.4706 (m-40) REVERT: H 109 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6704 (tm-30) REVERT: H 117 GLU cc_start: 0.6770 (mp0) cc_final: 0.5831 (mp0) REVERT: H 118 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6643 (mmpt) REVERT: H 143 GLU cc_start: 0.6593 (mt-10) cc_final: 0.6274 (mt-10) REVERT: H 216 ASP cc_start: 0.5424 (m-30) cc_final: 0.4710 (p0) REVERT: H 247 MET cc_start: 0.3839 (tmm) cc_final: 0.2494 (tpp) REVERT: H 278 ILE cc_start: 0.4789 (OUTLIER) cc_final: 0.4547 (mp) REVERT: H 372 ILE cc_start: 0.2616 (OUTLIER) cc_final: 0.2391 (pp) REVERT: H 402 ILE cc_start: 0.2943 (OUTLIER) cc_final: 0.2727 (pt) outliers start: 71 outliers final: 41 residues processed: 296 average time/residue: 0.5599 time to fit residues: 201.1876 Evaluate side-chains 264 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 606 GLU Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 468 LYS Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 372 ILE Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 402 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 58 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 176 optimal weight: 0.0770 chunk 70 optimal weight: 0.0270 chunk 196 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 145 optimal weight: 10.0000 chunk 300 optimal weight: 0.7980 chunk 308 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 205 optimal weight: 0.0770 overall best weight: 0.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 ASN D 463 ASN F 583 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.159061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121696 restraints weight = 132470.513| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 5.16 r_work: 0.2886 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31177 Z= 0.091 Angle : 0.493 14.460 42251 Z= 0.264 Chirality : 0.044 0.157 4758 Planarity : 0.004 0.057 5493 Dihedral : 4.493 42.932 4207 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.67 % Allowed : 10.80 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3884 helix: 1.21 (0.22), residues: 596 sheet: 0.93 (0.16), residues: 1192 loop : -0.85 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 77 TYR 0.015 0.001 TYR G 704 PHE 0.019 0.001 PHE C 711 TRP 0.012 0.001 TRP B 375 HIS 0.002 0.000 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00190 (31177) covalent geometry : angle 0.49299 (42251) hydrogen bonds : bond 0.02650 ( 1124) hydrogen bonds : angle 4.64405 ( 2979) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 254 time to evaluate : 1.272 Fit side-chains REVERT: A 305 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8387 (mt-10) REVERT: A 314 HIS cc_start: 0.7696 (m-70) cc_final: 0.7139 (t-90) REVERT: A 319 GLN cc_start: 0.7325 (pt0) cc_final: 0.7118 (tt0) REVERT: A 321 LYS cc_start: 0.6550 (ttpp) cc_final: 0.6027 (mtmt) REVERT: A 371 ASN cc_start: 0.6769 (p0) cc_final: 0.6285 (m-40) REVERT: A 376 ASN cc_start: 0.7912 (m-40) cc_final: 0.7335 (t0) REVERT: A 499 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7983 (tp30) REVERT: A 738 ILE cc_start: 0.7408 (mt) cc_final: 0.6875 (tp) REVERT: B 263 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 313 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7988 (mt-10) REVERT: B 582 ASP cc_start: 0.8086 (m-30) cc_final: 0.7640 (m-30) REVERT: C 218 ASP cc_start: 0.6551 (p0) cc_final: 0.6189 (m-30) REVERT: C 305 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: C 480 THR cc_start: 0.9033 (t) cc_final: 0.8774 (m) REVERT: C 536 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7481 (mp-120) REVERT: C 544 GLU cc_start: 0.8630 (tt0) cc_final: 0.8329 (mt-10) REVERT: C 569 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.8012 (mp) REVERT: C 582 ASP cc_start: 0.7946 (m-30) cc_final: 0.7675 (m-30) REVERT: C 589 LYS cc_start: 0.7988 (ttpp) cc_final: 0.7369 (ptpp) REVERT: C 655 LYS cc_start: 0.5554 (OUTLIER) cc_final: 0.5150 (mmtt) REVERT: C 711 PHE cc_start: 0.6511 (p90) cc_final: 0.6141 (p90) REVERT: D 314 HIS cc_start: 0.7534 (m-70) cc_final: 0.6958 (t70) REVERT: D 317 THR cc_start: 0.7956 (m) cc_final: 0.7753 (p) REVERT: D 318 ASP cc_start: 0.7072 (m-30) cc_final: 0.6816 (m-30) REVERT: D 382 ASN cc_start: 0.8559 (t0) cc_final: 0.8278 (t0) REVERT: D 458 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7044 (ttt-90) REVERT: D 660 MET cc_start: 0.5999 (tpt) cc_final: 0.5666 (tmt) REVERT: E 251 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7512 (mm-30) REVERT: E 252 GLN cc_start: 0.8024 (mt0) cc_final: 0.7556 (mm-40) REVERT: E 321 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6937 (ttmm) REVERT: E 376 ASN cc_start: 0.7743 (m-40) cc_final: 0.7392 (t0) REVERT: E 589 LYS cc_start: 0.8103 (ttpp) cc_final: 0.7832 (tttm) REVERT: E 707 PHE cc_start: 0.6380 (OUTLIER) cc_final: 0.5319 (p90) REVERT: E 711 PHE cc_start: 0.6879 (p90) cc_final: 0.6438 (p90) REVERT: F 321 LYS cc_start: 0.7078 (tttm) cc_final: 0.6826 (ttpp) REVERT: F 373 GLU cc_start: 0.6895 (pt0) cc_final: 0.6012 (pm20) REVERT: F 499 GLU cc_start: 0.8708 (tp30) cc_final: 0.8470 (tp30) REVERT: F 582 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7131 (t70) REVERT: F 722 GLU cc_start: 0.6278 (mm-30) cc_final: 0.6015 (tp30) REVERT: G 370 SER cc_start: 0.6670 (m) cc_final: 0.6261 (t) REVERT: G 376 ASN cc_start: 0.7576 (m-40) cc_final: 0.7284 (m-40) REVERT: G 382 ASN cc_start: 0.8778 (t0) cc_final: 0.8518 (t0) REVERT: G 582 ASP cc_start: 0.7947 (m-30) cc_final: 0.7661 (t0) REVERT: H 26 ARG cc_start: 0.4605 (tmm160) cc_final: 0.3568 (ttm110) REVERT: H 65 GLU cc_start: 0.4999 (mt-10) cc_final: 0.4343 (tp30) REVERT: H 77 ARG cc_start: 0.5669 (ttp80) cc_final: 0.5286 (tmm-80) REVERT: H 78 ASN cc_start: 0.5243 (m-40) cc_final: 0.4710 (m-40) REVERT: H 109 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6664 (tm-30) REVERT: H 117 GLU cc_start: 0.6520 (mp0) cc_final: 0.5760 (mp0) REVERT: H 143 GLU cc_start: 0.6469 (mt-10) cc_final: 0.6109 (mt-10) REVERT: H 216 ASP cc_start: 0.5382 (m-30) cc_final: 0.4680 (p0) REVERT: H 287 ILE cc_start: 0.4810 (mp) cc_final: 0.4471 (mm) REVERT: H 372 ILE cc_start: 0.2664 (OUTLIER) cc_final: 0.2386 (pp) outliers start: 53 outliers final: 26 residues processed: 290 average time/residue: 0.5455 time to fit residues: 192.5301 Evaluate side-chains 266 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 372 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 138 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 284 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 334 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN B 463 ASN E 392 ASN F 583 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.153105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114942 restraints weight = 154382.934| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 5.38 r_work: 0.2783 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 31177 Z= 0.296 Angle : 0.770 19.485 42251 Z= 0.416 Chirality : 0.054 0.243 4758 Planarity : 0.006 0.068 5493 Dihedral : 5.546 40.825 4207 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 2.66 % Allowed : 11.29 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 3884 helix: 0.55 (0.21), residues: 588 sheet: 0.53 (0.15), residues: 1184 loop : -1.03 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 232 TYR 0.037 0.003 TYR B 704 PHE 0.026 0.003 PHE A 711 TRP 0.019 0.002 TRP A 632 HIS 0.004 0.002 AHIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00717 (31177) covalent geometry : angle 0.76959 (42251) hydrogen bonds : bond 0.04954 ( 1124) hydrogen bonds : angle 5.35359 ( 2979) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 230 time to evaluate : 1.056 Fit side-chains REVERT: A 314 HIS cc_start: 0.7689 (m-70) cc_final: 0.7222 (t-90) REVERT: A 319 GLN cc_start: 0.7755 (pt0) cc_final: 0.7303 (pt0) REVERT: A 321 LYS cc_start: 0.6852 (ttpp) cc_final: 0.6364 (ttmt) REVERT: A 371 ASN cc_start: 0.6995 (p0) cc_final: 0.6612 (m-40) REVERT: A 376 ASN cc_start: 0.8005 (m-40) cc_final: 0.7507 (t0) REVERT: A 499 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8129 (tp30) REVERT: B 318 ASP cc_start: 0.7308 (m-30) cc_final: 0.6951 (m-30) REVERT: B 321 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6865 (ptpp) REVERT: B 582 ASP cc_start: 0.8260 (m-30) cc_final: 0.7819 (m-30) REVERT: C 218 ASP cc_start: 0.6573 (p0) cc_final: 0.6203 (m-30) REVERT: C 252 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7007 (mp10) REVERT: C 381 ILE cc_start: 0.8143 (tp) cc_final: 0.7739 (pt) REVERT: C 495 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7722 (tp40) REVERT: C 522 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7133 (tp30) REVERT: C 536 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7593 (mp-120) REVERT: C 544 GLU cc_start: 0.8640 (tt0) cc_final: 0.8386 (mt-10) REVERT: C 569 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8126 (mp) REVERT: C 582 ASP cc_start: 0.7901 (m-30) cc_final: 0.7671 (m-30) REVERT: C 621 ASN cc_start: 0.6871 (p0) cc_final: 0.6532 (p0) REVERT: C 655 LYS cc_start: 0.5824 (OUTLIER) cc_final: 0.5411 (mmtt) REVERT: C 710 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6524 (mt-10) REVERT: D 314 HIS cc_start: 0.7500 (m-70) cc_final: 0.6979 (t70) REVERT: D 458 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7107 (ttt-90) REVERT: D 660 MET cc_start: 0.5912 (tpt) cc_final: 0.5294 (tmt) REVERT: E 252 GLN cc_start: 0.8021 (mt0) cc_final: 0.7650 (mm-40) REVERT: E 589 LYS cc_start: 0.8144 (ttpp) cc_final: 0.7848 (tttm) REVERT: E 606 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8296 (mt-10) REVERT: E 660 MET cc_start: 0.6727 (tpt) cc_final: 0.6489 (tpt) REVERT: F 218 ASP cc_start: 0.7055 (p0) cc_final: 0.6807 (p0) REVERT: F 321 LYS cc_start: 0.7247 (tttm) cc_final: 0.6985 (ttpp) REVERT: F 568 ASP cc_start: 0.7551 (m-30) cc_final: 0.7316 (p0) REVERT: F 583 ASN cc_start: 0.8276 (m110) cc_final: 0.7664 (t0) REVERT: F 706 LYS cc_start: 0.5858 (mtmt) cc_final: 0.5492 (mtmt) REVERT: F 722 GLU cc_start: 0.6262 (mm-30) cc_final: 0.5771 (mm-30) REVERT: G 218 ASP cc_start: 0.7413 (t70) cc_final: 0.7180 (t70) REVERT: G 426 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: G 583 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7602 (t0) REVERT: H 26 ARG cc_start: 0.4305 (tmm160) cc_final: 0.3290 (ttm110) REVERT: H 65 GLU cc_start: 0.4778 (mt-10) cc_final: 0.4238 (tp30) REVERT: H 77 ARG cc_start: 0.6012 (ttp80) cc_final: 0.5572 (ttp80) REVERT: H 78 ASN cc_start: 0.4816 (m-40) cc_final: 0.4431 (m-40) REVERT: H 104 LYS cc_start: 0.4954 (mtpp) cc_final: 0.4750 (mmmt) REVERT: H 109 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6806 (tm-30) REVERT: H 143 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6402 (mt-10) REVERT: H 180 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: H 216 ASP cc_start: 0.5440 (m-30) cc_final: 0.4715 (p0) REVERT: H 247 MET cc_start: 0.3550 (tmm) cc_final: 0.2404 (tpp) REVERT: H 299 PRO cc_start: 0.3414 (Cg_exo) cc_final: 0.3024 (Cg_endo) REVERT: H 372 ILE cc_start: 0.2710 (OUTLIER) cc_final: 0.2495 (mp) REVERT: H 402 ILE cc_start: 0.2921 (OUTLIER) cc_final: 0.2653 (pt) outliers start: 89 outliers final: 53 residues processed: 298 average time/residue: 0.5582 time to fit residues: 201.1158 Evaluate side-chains 268 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 522 GLU Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 672 SER Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 606 GLU Chi-restraints excluded: chain E residue 658 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 583 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 314 ASN Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 372 ILE Chi-restraints excluded: chain H residue 387 SER Chi-restraints excluded: chain H residue 402 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 364 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 290 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 356 optimal weight: 0.0470 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN B 312 ASN D 495 GLN B E 523 ASN E 602 ASN E 634 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.155737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118790 restraints weight = 143478.225| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 5.28 r_work: 0.2825 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31177 Z= 0.129 Angle : 0.564 16.455 42251 Z= 0.302 Chirality : 0.045 0.165 4758 Planarity : 0.004 0.063 5493 Dihedral : 4.950 41.219 4207 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.02 % Allowed : 12.56 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 3884 helix: 0.95 (0.22), residues: 590 sheet: 0.89 (0.15), residues: 1205 loop : -1.01 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 77 TYR 0.020 0.001 TYR B 704 PHE 0.018 0.001 PHE C 711 TRP 0.015 0.001 TRP B 375 HIS 0.003 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00292 (31177) covalent geometry : angle 0.56416 (42251) hydrogen bonds : bond 0.03273 ( 1124) hydrogen bonds : angle 4.88073 ( 2979) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 223 time to evaluate : 1.072 Fit side-chains REVERT: A 314 HIS cc_start: 0.7561 (m-70) cc_final: 0.7149 (t-90) REVERT: A 319 GLN cc_start: 0.7442 (pt0) cc_final: 0.7083 (tt0) REVERT: A 321 LYS cc_start: 0.6734 (ttpp) cc_final: 0.6166 (mtmt) REVERT: A 376 ASN cc_start: 0.8027 (m-40) cc_final: 0.7406 (t0) REVERT: A 499 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8024 (tp30) REVERT: A 544 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: B 318 ASP cc_start: 0.7289 (m-30) cc_final: 0.6907 (m-30) REVERT: B 582 ASP cc_start: 0.8204 (m-30) cc_final: 0.7773 (m-30) REVERT: B 701 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5854 (mp0) REVERT: C 218 ASP cc_start: 0.6514 (p0) cc_final: 0.6185 (m-30) REVERT: C 252 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.6999 (mp10) REVERT: C 370 SER cc_start: 0.6482 (m) cc_final: 0.6230 (p) REVERT: C 381 ILE cc_start: 0.8081 (tp) cc_final: 0.7666 (pt) REVERT: C 495 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7724 (tp40) REVERT: C 536 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7539 (mp-120) REVERT: C 544 GLU cc_start: 0.8660 (tt0) cc_final: 0.8390 (mt-10) REVERT: C 569 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8141 (mp) REVERT: C 582 ASP cc_start: 0.7877 (m-30) cc_final: 0.7577 (m-30) REVERT: C 589 LYS cc_start: 0.7959 (ptmm) cc_final: 0.7537 (pttm) REVERT: C 655 LYS cc_start: 0.5760 (OUTLIER) cc_final: 0.5381 (mmtt) REVERT: C 710 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6565 (mt-10) REVERT: D 314 HIS cc_start: 0.7411 (m-70) cc_final: 0.6921 (t70) REVERT: D 382 ASN cc_start: 0.8530 (t0) cc_final: 0.8248 (t0) REVERT: D 458 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7118 (ttt-90) REVERT: D 660 MET cc_start: 0.6092 (tpt) cc_final: 0.5574 (tmt) REVERT: D 689 LYS cc_start: 0.5950 (tmtt) cc_final: 0.5433 (ttpp) REVERT: E 252 GLN cc_start: 0.7877 (mt0) cc_final: 0.7544 (mm-40) REVERT: E 321 LYS cc_start: 0.7120 (ttpt) cc_final: 0.6507 (tttt) REVERT: E 589 LYS cc_start: 0.8061 (ttpp) cc_final: 0.7767 (tttm) REVERT: E 660 MET cc_start: 0.6798 (tpt) cc_final: 0.6445 (tpt) REVERT: F 218 ASP cc_start: 0.7033 (p0) cc_final: 0.6711 (p0) REVERT: F 373 GLU cc_start: 0.6995 (pt0) cc_final: 0.6774 (pt0) REVERT: F 568 ASP cc_start: 0.7534 (m-30) cc_final: 0.7319 (p0) REVERT: F 583 ASN cc_start: 0.8206 (m110) cc_final: 0.7595 (t0) REVERT: F 706 LYS cc_start: 0.5674 (mtmt) cc_final: 0.5280 (mtmt) REVERT: F 722 GLU cc_start: 0.6027 (mm-30) cc_final: 0.5627 (mm-30) REVERT: F 739 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7403 (m) REVERT: G 370 SER cc_start: 0.6817 (m) cc_final: 0.6360 (t) REVERT: G 426 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: H 26 ARG cc_start: 0.4003 (tmm160) cc_final: 0.3041 (ttm110) REVERT: H 60 TYR cc_start: 0.4396 (m-80) cc_final: 0.2967 (t80) REVERT: H 65 GLU cc_start: 0.4847 (mt-10) cc_final: 0.4294 (mm-30) REVERT: H 77 ARG cc_start: 0.5943 (ttp80) cc_final: 0.5458 (ttp80) REVERT: H 78 ASN cc_start: 0.4874 (m-40) cc_final: 0.4442 (m-40) REVERT: H 109 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6700 (tm-30) REVERT: H 117 GLU cc_start: 0.6815 (mp0) cc_final: 0.6163 (mp0) REVERT: H 143 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6392 (mt-10) REVERT: H 180 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: H 216 ASP cc_start: 0.5462 (m-30) cc_final: 0.4788 (p0) REVERT: H 247 MET cc_start: 0.3649 (tmm) cc_final: 0.2304 (tpp) REVERT: H 372 ILE cc_start: 0.2776 (OUTLIER) cc_final: 0.2548 (pp) REVERT: H 402 ILE cc_start: 0.2969 (OUTLIER) cc_final: 0.2760 (pt) outliers start: 67 outliers final: 40 residues processed: 273 average time/residue: 0.5561 time to fit residues: 183.8765 Evaluate side-chains 262 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 372 ILE Chi-restraints excluded: chain H residue 402 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 6 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 338 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 311 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 195 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 285 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 627 ASN H 157 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.156661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119820 restraints weight = 130029.578| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 5.14 r_work: 0.2843 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 31177 Z= 0.108 Angle : 0.528 15.167 42251 Z= 0.284 Chirality : 0.044 0.165 4758 Planarity : 0.004 0.062 5493 Dihedral : 4.736 39.942 4207 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.14 % Allowed : 12.73 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3884 helix: 1.11 (0.22), residues: 596 sheet: 0.93 (0.15), residues: 1181 loop : -0.94 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 77 TYR 0.029 0.001 TYR H 246 PHE 0.017 0.001 PHE C 711 TRP 0.021 0.001 TRP B 375 HIS 0.002 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00239 (31177) covalent geometry : angle 0.52816 (42251) hydrogen bonds : bond 0.02966 ( 1124) hydrogen bonds : angle 4.67614 ( 2979) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 223 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 314 HIS cc_start: 0.7559 (m-70) cc_final: 0.7170 (t-90) REVERT: A 319 GLN cc_start: 0.7378 (pt0) cc_final: 0.7100 (tt0) REVERT: A 321 LYS cc_start: 0.6827 (ttpp) cc_final: 0.6226 (mtmt) REVERT: A 376 ASN cc_start: 0.8058 (m-40) cc_final: 0.7446 (t0) REVERT: A 499 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8047 (tp30) REVERT: A 544 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: B 318 ASP cc_start: 0.7347 (m-30) cc_final: 0.6937 (m-30) REVERT: B 582 ASP cc_start: 0.8182 (m-30) cc_final: 0.7722 (m-30) REVERT: B 701 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5909 (mp0) REVERT: C 218 ASP cc_start: 0.6551 (p0) cc_final: 0.6245 (m-30) REVERT: C 252 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7052 (mp10) REVERT: C 318 ASP cc_start: 0.7303 (m-30) cc_final: 0.6992 (t70) REVERT: C 381 ILE cc_start: 0.8105 (tp) cc_final: 0.7706 (pt) REVERT: C 495 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7746 (tp40) REVERT: C 536 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7540 (mp-120) REVERT: C 544 GLU cc_start: 0.8664 (tt0) cc_final: 0.8397 (mt-10) REVERT: C 582 ASP cc_start: 0.7912 (m-30) cc_final: 0.7625 (m-30) REVERT: C 655 LYS cc_start: 0.5715 (OUTLIER) cc_final: 0.5346 (mmtt) REVERT: C 670 VAL cc_start: 0.7927 (t) cc_final: 0.7626 (p) REVERT: C 710 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6496 (mt-10) REVERT: D 314 HIS cc_start: 0.7407 (m-70) cc_final: 0.6940 (t70) REVERT: D 317 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7768 (p) REVERT: D 382 ASN cc_start: 0.8605 (t0) cc_final: 0.8310 (t0) REVERT: D 452 MET cc_start: 0.9007 (ptt) cc_final: 0.8758 (ptt) REVERT: D 458 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7196 (ttt-90) REVERT: D 660 MET cc_start: 0.6082 (tpt) cc_final: 0.5530 (tmt) REVERT: E 252 GLN cc_start: 0.7836 (mt0) cc_final: 0.7569 (mm-40) REVERT: E 321 LYS cc_start: 0.7270 (ttpt) cc_final: 0.6578 (tttt) REVERT: E 376 ASN cc_start: 0.7843 (m-40) cc_final: 0.7339 (t0) REVERT: E 589 LYS cc_start: 0.8083 (ttpp) cc_final: 0.7792 (tttm) REVERT: E 660 MET cc_start: 0.6759 (tpt) cc_final: 0.6402 (tpt) REVERT: F 373 GLU cc_start: 0.6918 (pt0) cc_final: 0.6687 (pt0) REVERT: F 583 ASN cc_start: 0.8203 (m110) cc_final: 0.7575 (t0) REVERT: F 722 GLU cc_start: 0.5898 (mm-30) cc_final: 0.5491 (mm-30) REVERT: F 739 THR cc_start: 0.7695 (OUTLIER) cc_final: 0.7473 (m) REVERT: G 370 SER cc_start: 0.6793 (m) cc_final: 0.6357 (t) REVERT: G 426 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: G 468 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8465 (mmtm) REVERT: H 26 ARG cc_start: 0.4124 (tmm160) cc_final: 0.3235 (ttm110) REVERT: H 33 ARG cc_start: 0.3749 (ptm-80) cc_final: 0.2878 (ptp-110) REVERT: H 65 GLU cc_start: 0.4821 (mt-10) cc_final: 0.4268 (mm-30) REVERT: H 77 ARG cc_start: 0.5942 (ttp80) cc_final: 0.5502 (tmm-80) REVERT: H 78 ASN cc_start: 0.4856 (m-40) cc_final: 0.4426 (m-40) REVERT: H 109 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6723 (tm-30) REVERT: H 117 GLU cc_start: 0.6819 (mp0) cc_final: 0.5967 (mp0) REVERT: H 143 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6332 (mt-10) REVERT: H 180 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: H 216 ASP cc_start: 0.5488 (m-30) cc_final: 0.4808 (p0) REVERT: H 247 MET cc_start: 0.3464 (tmm) cc_final: 0.2369 (tpp) REVERT: H 372 ILE cc_start: 0.2720 (OUTLIER) cc_final: 0.2492 (pp) outliers start: 70 outliers final: 43 residues processed: 278 average time/residue: 0.5670 time to fit residues: 190.3823 Evaluate side-chains 264 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 672 SER Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 658 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 468 LYS Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 372 ILE Chi-restraints excluded: chain H residue 387 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 244 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 chunk 352 optimal weight: 5.9990 chunk 372 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 627 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.155461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118301 restraints weight = 141116.176| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 5.20 r_work: 0.2819 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 31177 Z= 0.144 Angle : 0.574 16.296 42251 Z= 0.309 Chirality : 0.046 0.161 4758 Planarity : 0.004 0.062 5493 Dihedral : 4.923 40.988 4207 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.31 % Allowed : 12.99 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 3884 helix: 0.95 (0.22), residues: 596 sheet: 0.81 (0.15), residues: 1187 loop : -0.98 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 394 TYR 0.021 0.002 TYR E 439 PHE 0.015 0.002 PHE C 711 TRP 0.021 0.001 TRP B 375 HIS 0.005 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00337 (31177) covalent geometry : angle 0.57419 (42251) hydrogen bonds : bond 0.03439 ( 1124) hydrogen bonds : angle 4.81082 ( 2979) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 209 time to evaluate : 0.996 Fit side-chains REVERT: A 314 HIS cc_start: 0.7566 (m-70) cc_final: 0.7122 (t-90) REVERT: A 319 GLN cc_start: 0.7361 (pt0) cc_final: 0.7068 (tt0) REVERT: A 321 LYS cc_start: 0.6779 (ttpp) cc_final: 0.6180 (mtmt) REVERT: A 376 ASN cc_start: 0.8029 (m-40) cc_final: 0.7398 (t0) REVERT: A 499 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8099 (tp30) REVERT: B 318 ASP cc_start: 0.7294 (m-30) cc_final: 0.6870 (m-30) REVERT: B 582 ASP cc_start: 0.8207 (m-30) cc_final: 0.7789 (m-30) REVERT: B 701 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6002 (mp0) REVERT: C 218 ASP cc_start: 0.6534 (p0) cc_final: 0.6228 (m-30) REVERT: C 252 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.6994 (mp10) REVERT: C 381 ILE cc_start: 0.8074 (tp) cc_final: 0.7669 (pt) REVERT: C 495 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7728 (tp40) REVERT: C 522 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7079 (tp30) REVERT: C 536 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7514 (mp-120) REVERT: C 544 GLU cc_start: 0.8653 (tt0) cc_final: 0.8382 (mt-10) REVERT: C 582 ASP cc_start: 0.7896 (m-30) cc_final: 0.7593 (m-30) REVERT: C 655 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5354 (mmtt) REVERT: C 670 VAL cc_start: 0.7943 (t) cc_final: 0.7635 (p) REVERT: C 701 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5983 (mp0) REVERT: C 710 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6425 (mt-10) REVERT: D 305 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: D 314 HIS cc_start: 0.7422 (m-70) cc_final: 0.6910 (t70) REVERT: D 452 MET cc_start: 0.9114 (ptt) cc_final: 0.8895 (ptt) REVERT: D 458 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7085 (ttt-90) REVERT: D 660 MET cc_start: 0.5993 (tpt) cc_final: 0.5506 (tmt) REVERT: E 252 GLN cc_start: 0.7773 (mt0) cc_final: 0.7533 (mm-40) REVERT: E 321 LYS cc_start: 0.7188 (ttpt) cc_final: 0.6548 (tttt) REVERT: E 376 ASN cc_start: 0.7776 (m-40) cc_final: 0.7279 (t0) REVERT: E 589 LYS cc_start: 0.8046 (ttpp) cc_final: 0.7754 (tttm) REVERT: E 660 MET cc_start: 0.6737 (tpt) cc_final: 0.6440 (tpt) REVERT: F 373 GLU cc_start: 0.6951 (pt0) cc_final: 0.6719 (pt0) REVERT: F 583 ASN cc_start: 0.8191 (m110) cc_final: 0.7586 (t0) REVERT: F 707 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.3676 (p90) REVERT: F 722 GLU cc_start: 0.5864 (mm-30) cc_final: 0.5399 (mm-30) REVERT: G 426 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: G 468 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8430 (mmtm) REVERT: H 26 ARG cc_start: 0.4043 (tmm160) cc_final: 0.3108 (ttm110) REVERT: H 30 LYS cc_start: 0.5288 (mmmt) cc_final: 0.4912 (mtpt) REVERT: H 33 ARG cc_start: 0.3803 (ptm-80) cc_final: 0.2928 (ptp-110) REVERT: H 51 LYS cc_start: 0.5167 (OUTLIER) cc_final: 0.4747 (mtpt) REVERT: H 65 GLU cc_start: 0.4898 (mt-10) cc_final: 0.4291 (mm-30) REVERT: H 77 ARG cc_start: 0.5896 (ttp80) cc_final: 0.5471 (ttp80) REVERT: H 78 ASN cc_start: 0.4797 (m-40) cc_final: 0.4386 (m-40) REVERT: H 109 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6703 (tm-30) REVERT: H 143 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6415 (mt-10) REVERT: H 180 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: H 216 ASP cc_start: 0.5438 (m-30) cc_final: 0.4774 (p0) REVERT: H 240 LEU cc_start: 0.4815 (tp) cc_final: 0.4610 (tp) REVERT: H 247 MET cc_start: 0.3320 (tmm) cc_final: 0.2394 (tpp) outliers start: 76 outliers final: 52 residues processed: 272 average time/residue: 0.5689 time to fit residues: 186.9774 Evaluate side-chains 272 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 522 GLU Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 672 SER Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 658 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 468 LYS Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 387 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 372 optimal weight: 0.0370 chunk 337 optimal weight: 4.9990 chunk 375 optimal weight: 0.0070 chunk 184 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 133 optimal weight: 0.3980 chunk 124 optimal weight: 0.5980 chunk 324 optimal weight: 1.9990 chunk 300 optimal weight: 0.0070 chunk 291 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 627 ASN E 265 ASN H 385 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.158485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122194 restraints weight = 140091.622| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 5.16 r_work: 0.2886 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31177 Z= 0.091 Angle : 0.489 13.708 42251 Z= 0.261 Chirality : 0.043 0.160 4758 Planarity : 0.004 0.059 5493 Dihedral : 4.467 40.579 4207 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.41 % Allowed : 13.80 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3884 helix: 1.18 (0.22), residues: 596 sheet: 1.27 (0.16), residues: 1163 loop : -0.89 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 77 TYR 0.023 0.001 TYR H 246 PHE 0.015 0.001 PHE C 711 TRP 0.024 0.001 TRP B 375 HIS 0.004 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00193 (31177) covalent geometry : angle 0.48867 (42251) hydrogen bonds : bond 0.02380 ( 1124) hydrogen bonds : angle 4.48335 ( 2979) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 314 HIS cc_start: 0.7554 (m-70) cc_final: 0.7133 (t-90) REVERT: A 321 LYS cc_start: 0.6905 (ttpp) cc_final: 0.6286 (mtmt) REVERT: A 376 ASN cc_start: 0.7920 (m-40) cc_final: 0.7350 (t0) REVERT: A 480 THR cc_start: 0.9152 (t) cc_final: 0.8848 (m) REVERT: B 305 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8541 (mt-10) REVERT: B 318 ASP cc_start: 0.7345 (m-30) cc_final: 0.6931 (m-30) REVERT: B 582 ASP cc_start: 0.8084 (m-30) cc_final: 0.7669 (m-30) REVERT: C 218 ASP cc_start: 0.6482 (p0) cc_final: 0.6195 (m-30) REVERT: C 252 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.6897 (mp10) REVERT: C 318 ASP cc_start: 0.7332 (m-30) cc_final: 0.7027 (t70) REVERT: C 480 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8795 (m) REVERT: C 536 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7483 (mp-120) REVERT: C 544 GLU cc_start: 0.8668 (tt0) cc_final: 0.8398 (mt-10) REVERT: C 582 ASP cc_start: 0.7944 (m-30) cc_final: 0.7675 (m-30) REVERT: C 670 VAL cc_start: 0.7892 (t) cc_final: 0.7570 (p) REVERT: D 305 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: D 314 HIS cc_start: 0.7392 (m-70) cc_final: 0.6890 (t70) REVERT: D 382 ASN cc_start: 0.8548 (t0) cc_final: 0.8314 (t0) REVERT: D 452 MET cc_start: 0.8941 (ptt) cc_final: 0.8717 (ptt) REVERT: D 458 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7047 (ttt-90) REVERT: D 660 MET cc_start: 0.5965 (tpt) cc_final: 0.5499 (tmt) REVERT: D 689 LYS cc_start: 0.5853 (tptt) cc_final: 0.5433 (tmtt) REVERT: E 321 LYS cc_start: 0.7126 (ttpt) cc_final: 0.6909 (ttmm) REVERT: E 376 ASN cc_start: 0.7917 (m-40) cc_final: 0.7415 (t0) REVERT: E 589 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7786 (tttm) REVERT: E 660 MET cc_start: 0.6575 (tpt) cc_final: 0.6216 (tpt) REVERT: F 319 GLN cc_start: 0.7625 (pt0) cc_final: 0.7132 (mt0) REVERT: F 373 GLU cc_start: 0.6882 (pt0) cc_final: 0.6656 (pt0) REVERT: F 499 GLU cc_start: 0.8693 (tp30) cc_final: 0.8466 (tp30) REVERT: F 583 ASN cc_start: 0.8149 (m110) cc_final: 0.7507 (t0) REVERT: G 382 ASN cc_start: 0.8795 (t0) cc_final: 0.8562 (t0) REVERT: H 26 ARG cc_start: 0.4114 (tmm160) cc_final: 0.3211 (ttm110) REVERT: H 33 ARG cc_start: 0.3783 (ptm-80) cc_final: 0.3240 (ptp-110) REVERT: H 60 TYR cc_start: 0.4327 (m-80) cc_final: 0.2960 (t80) REVERT: H 65 GLU cc_start: 0.4869 (mt-10) cc_final: 0.4240 (mm-30) REVERT: H 74 LYS cc_start: 0.6151 (mttm) cc_final: 0.5906 (mmmm) REVERT: H 77 ARG cc_start: 0.5952 (ttp80) cc_final: 0.5594 (tmm-80) REVERT: H 78 ASN cc_start: 0.4885 (m-40) cc_final: 0.4457 (m-40) REVERT: H 109 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6663 (tm-30) REVERT: H 143 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6298 (mt-10) REVERT: H 216 ASP cc_start: 0.5467 (m-30) cc_final: 0.4783 (p0) REVERT: H 247 MET cc_start: 0.3316 (tmm) cc_final: 0.2492 (tpp) outliers start: 45 outliers final: 28 residues processed: 275 average time/residue: 0.5529 time to fit residues: 184.1457 Evaluate side-chains 253 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 658 ILE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 339 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 336 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 chunk 349 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 370 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN C 627 ASN E 252 GLN H 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.155034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117552 restraints weight = 143779.703| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 5.21 r_work: 0.2818 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 31177 Z= 0.172 Angle : 0.604 16.661 42251 Z= 0.326 Chirality : 0.047 0.151 4758 Planarity : 0.004 0.061 5493 Dihedral : 4.941 40.589 4207 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.39 % Allowed : 13.97 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 3884 helix: 0.96 (0.22), residues: 596 sheet: 0.86 (0.16), residues: 1189 loop : -0.97 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 529 TYR 0.022 0.002 TYR E 439 PHE 0.015 0.002 PHE A 711 TRP 0.025 0.001 TRP B 375 HIS 0.005 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00409 (31177) covalent geometry : angle 0.60379 (42251) hydrogen bonds : bond 0.03627 ( 1124) hydrogen bonds : angle 4.80390 ( 2979) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 1.144 Fit side-chains REVERT: A 314 HIS cc_start: 0.7594 (m-70) cc_final: 0.7126 (t-90) REVERT: A 321 LYS cc_start: 0.6958 (ttpp) cc_final: 0.6282 (mtmp) REVERT: A 376 ASN cc_start: 0.7970 (m-40) cc_final: 0.7410 (t0) REVERT: A 499 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8073 (tp30) REVERT: B 318 ASP cc_start: 0.7312 (m-30) cc_final: 0.6893 (m-30) REVERT: B 371 ASN cc_start: 0.7063 (m-40) cc_final: 0.6831 (m-40) REVERT: B 582 ASP cc_start: 0.8211 (m-30) cc_final: 0.7759 (m-30) REVERT: C 218 ASP cc_start: 0.6530 (p0) cc_final: 0.6255 (m-30) REVERT: C 252 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.6998 (mp10) REVERT: C 381 ILE cc_start: 0.8065 (tp) cc_final: 0.7655 (pt) REVERT: C 536 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7508 (mp-120) REVERT: C 544 GLU cc_start: 0.8638 (tt0) cc_final: 0.8369 (mt-10) REVERT: C 582 ASP cc_start: 0.7878 (m-30) cc_final: 0.7576 (m-30) REVERT: C 710 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6394 (mt-10) REVERT: D 217 GLU cc_start: 0.5991 (pp20) cc_final: 0.5753 (pp20) REVERT: D 314 HIS cc_start: 0.7418 (m-70) cc_final: 0.6944 (t70) REVERT: D 452 MET cc_start: 0.9129 (ptt) cc_final: 0.8914 (ptt) REVERT: D 458 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7081 (ttt-90) REVERT: D 660 MET cc_start: 0.5948 (tpt) cc_final: 0.5508 (tmt) REVERT: E 321 LYS cc_start: 0.7197 (ttpt) cc_final: 0.6497 (tttt) REVERT: E 376 ASN cc_start: 0.7919 (m-40) cc_final: 0.7380 (t0) REVERT: E 589 LYS cc_start: 0.8119 (ttpp) cc_final: 0.7801 (tttm) REVERT: E 646 SER cc_start: 0.7095 (t) cc_final: 0.6450 (p) REVERT: E 660 MET cc_start: 0.6796 (tpt) cc_final: 0.6541 (tpt) REVERT: F 371 ASN cc_start: 0.6851 (OUTLIER) cc_final: 0.6531 (m110) REVERT: F 373 GLU cc_start: 0.7005 (pt0) cc_final: 0.6776 (pt0) REVERT: F 563 LEU cc_start: 0.7753 (mt) cc_final: 0.7515 (mt) REVERT: F 583 ASN cc_start: 0.8178 (m110) cc_final: 0.7587 (t0) REVERT: F 706 LYS cc_start: 0.5868 (mtmt) cc_final: 0.5521 (mtmt) REVERT: F 707 PHE cc_start: 0.5976 (OUTLIER) cc_final: 0.3465 (p90) REVERT: G 218 ASP cc_start: 0.7398 (t70) cc_final: 0.7187 (t70) REVERT: G 426 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: G 468 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8471 (mmtm) REVERT: H 26 ARG cc_start: 0.4123 (tmm160) cc_final: 0.3094 (ttm110) REVERT: H 30 LYS cc_start: 0.5284 (mmmt) cc_final: 0.4925 (mtpt) REVERT: H 33 ARG cc_start: 0.3956 (ptm-80) cc_final: 0.3064 (ptp-110) REVERT: H 60 TYR cc_start: 0.4289 (m-80) cc_final: 0.2907 (t80) REVERT: H 65 GLU cc_start: 0.4914 (mt-10) cc_final: 0.4248 (mm-30) REVERT: H 77 ARG cc_start: 0.5867 (ttp80) cc_final: 0.5432 (ttp80) REVERT: H 78 ASN cc_start: 0.4820 (m-40) cc_final: 0.4430 (m-40) REVERT: H 109 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6715 (tm-30) REVERT: H 143 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6414 (mt-10) REVERT: H 180 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: H 216 ASP cc_start: 0.5442 (m-30) cc_final: 0.4797 (p0) REVERT: H 247 MET cc_start: 0.3509 (tmm) cc_final: 0.2506 (tpp) REVERT: H 372 ILE cc_start: 0.2663 (OUTLIER) cc_final: 0.2450 (mp) outliers start: 44 outliers final: 31 residues processed: 253 average time/residue: 0.5643 time to fit residues: 172.9598 Evaluate side-chains 250 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 594 THR Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 658 ILE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 468 LYS Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 372 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 370 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 264 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 627 ASN H 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.155677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118454 restraints weight = 149696.332| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 5.23 r_work: 0.2824 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31177 Z= 0.128 Angle : 0.564 16.007 42251 Z= 0.304 Chirality : 0.045 0.158 4758 Planarity : 0.004 0.060 5493 Dihedral : 4.857 40.845 4207 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.50 % Allowed : 13.97 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3884 helix: 0.99 (0.22), residues: 596 sheet: 0.84 (0.16), residues: 1189 loop : -0.97 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 352 TYR 0.025 0.002 TYR H 251 PHE 0.015 0.002 PHE C 711 TRP 0.025 0.001 TRP B 375 HIS 0.004 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00293 (31177) covalent geometry : angle 0.56352 (42251) hydrogen bonds : bond 0.03257 ( 1124) hydrogen bonds : angle 4.75134 ( 2979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13349.01 seconds wall clock time: 227 minutes 9.53 seconds (13629.53 seconds total)