Starting phenix.real_space_refine on Wed Feb 21 12:49:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnj_32041/02_2024/7vnj_32041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnj_32041/02_2024/7vnj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnj_32041/02_2024/7vnj_32041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnj_32041/02_2024/7vnj_32041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnj_32041/02_2024/7vnj_32041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnj_32041/02_2024/7vnj_32041.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 24.23, per 1000 atoms: 0.79 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 - 3.50 Amino acid : False - 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: 12.59 Conformation dependent library (CDL) restraints added in 9.5 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: 3.91 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: 14.19 Time building geometry restraints manager: 13.41 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: 100.13 - 106.91: 667 106.91 - 113.69: 17423 113.69 - 120.47: 11485 120.47 - 127.25: 12495 127.25 - 134.03: 181 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 2.440 nonbonded pdb=" NH2 ARG D 394 " pdb=" O LEU D 444 " model vdw 2.216 2.520 nonbonded pdb=" NH2 ARG B 394 " pdb=" O LEU B 444 " model vdw 2.234 2.520 nonbonded pdb=" NH2 ARG F 394 " pdb=" O LEU F 444 " model vdw 2.235 2.520 nonbonded pdb=" NH2 ARG C 394 " pdb=" O LEU C 444 " model vdw 2.241 2.520 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'B' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'C' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'D' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'E' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'F' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'G' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 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: 3.740 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: 0.040 Extract box with map and model: 17.880 Check model and map are aligned: 0.610 Set scattering table: 0.340 Process input model: 96.890 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.200 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:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.240 ------------------------------------------------------------------------------- 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= 0.206 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (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 TRP 0.015 0.001 TRP D 214 HIS 0.001 0.000 AHIS A 314 PHE 0.012 0.001 PHE B 707 TYR 0.017 0.001 TYR G 704 ARG 0.005 0.000 ARG H 33 *********************** 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 fitting. rotamer outliers: 8 poor density : 477 time to evaluate : 3.414 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: 0.6516 (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: 0.6178 (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: 0.7921 (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: 0.7215 (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: 0.6368 (mt0) REVERT: E 321 LYS cc_start: 0.6133 (ttpt) cc_final: 0.5573 (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: 0.5679 (mt0) 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: 0.7265 (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: 0.4066 (tp30) REVERT: H 78 ASN cc_start: 0.4854 (m-40) cc_final: 0.4255 (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: 0.5053 (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: 0.3414 (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: 1.3129 time to fit residues: 758.7862 Evaluate side-chains 262 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 253 time to evaluate : 3.371 ------------------------------------------------------------------------------- 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 322 optimal weight: 2.9990 chunk 289 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 195 optimal weight: 8.9990 chunk 154 optimal weight: 0.6980 chunk 299 optimal weight: 3.9990 chunk 115 optimal weight: 0.0070 chunk 182 optimal weight: 1.9990 chunk 222 optimal weight: 0.5980 chunk 346 optimal weight: 5.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 602 ASN C 610 ASN D 371 ASN D 463 ASN D 735 ASN E 475 GLN E 602 ASN F 392 ASN F 583 ASN G 392 ASN G 501 ASN H 157 HIS H 244 ASN H 384 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31177 Z= 0.164 Angle : 0.547 15.713 42251 Z= 0.292 Chirality : 0.046 0.192 4758 Planarity : 0.004 0.060 5493 Dihedral : 4.574 41.913 4211 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.88 % Allowed : 7.42 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3884 helix: 1.09 (0.22), residues: 602 sheet: 0.63 (0.15), residues: 1234 loop : -0.84 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 245 HIS 0.003 0.001 HIS H 157 PHE 0.012 0.002 PHE F 487 TYR 0.038 0.001 TYR H 246 ARG 0.008 0.001 ARG E 394 *********************** 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 350 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 291 time to evaluate : 3.541 Fit side-chains REVERT: A 269 ASP cc_start: 0.7874 (p0) cc_final: 0.7516 (p0) REVERT: A 319 GLN cc_start: 0.6717 (pt0) cc_final: 0.6217 (pt0) REVERT: A 321 LYS cc_start: 0.5623 (ttpp) cc_final: 0.5069 (ttpt) REVERT: A 376 ASN cc_start: 0.7114 (m-40) cc_final: 0.6478 (t0) REVERT: A 385 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6903 (mp0) REVERT: A 452 MET cc_start: 0.8822 (ptt) cc_final: 0.8589 (ptt) REVERT: B 269 ASP cc_start: 0.7871 (p0) cc_final: 0.7625 (p0) REVERT: B 313 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7284 (mt-10) REVERT: B 318 ASP cc_start: 0.6298 (m-30) cc_final: 0.5877 (m-30) REVERT: B 319 GLN cc_start: 0.6934 (tt0) cc_final: 0.6656 (tt0) REVERT: B 426 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7102 (pm20) REVERT: B 582 ASP cc_start: 0.7828 (m-30) cc_final: 0.7169 (m-30) REVERT: B 586 ASN cc_start: 0.7495 (m-40) cc_final: 0.7251 (m110) REVERT: C 313 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7131 (mt-10) REVERT: C 314 HIS cc_start: 0.6864 (m-70) cc_final: 0.5858 (t-170) REVERT: C 544 GLU cc_start: 0.7516 (tt0) cc_final: 0.7139 (tt0) REVERT: C 569 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7657 (mp) REVERT: C 582 ASP cc_start: 0.7458 (m-30) cc_final: 0.7056 (m-30) REVERT: C 589 LYS cc_start: 0.7769 (ttpp) cc_final: 0.7347 (ttmm) REVERT: C 621 ASN cc_start: 0.6349 (p0) cc_final: 0.6137 (p0) REVERT: C 660 MET cc_start: 0.6414 (tpt) cc_final: 0.6109 (mmt) REVERT: D 290 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7329 (mtp180) REVERT: D 318 ASP cc_start: 0.6112 (m-30) cc_final: 0.5762 (m-30) REVERT: D 376 ASN cc_start: 0.7247 (m-40) cc_final: 0.7010 (m-40) REVERT: D 382 ASN cc_start: 0.8191 (t0) cc_final: 0.7880 (t0) REVERT: D 458 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.6690 (ttt-90) REVERT: D 568 ASP cc_start: 0.6463 (m-30) cc_final: 0.6239 (m-30) REVERT: D 660 MET cc_start: 0.5518 (tpt) cc_final: 0.5113 (tmt) REVERT: E 252 GLN cc_start: 0.7702 (mt0) cc_final: 0.6895 (mm-40) REVERT: E 313 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6636 (mt-10) REVERT: E 321 LYS cc_start: 0.6331 (ttpt) cc_final: 0.5642 (tttt) REVERT: E 373 GLU cc_start: 0.6172 (pt0) cc_final: 0.5930 (pt0) REVERT: E 376 ASN cc_start: 0.6560 (m-40) cc_final: 0.6268 (t0) REVERT: E 606 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7355 (mt-10) REVERT: E 707 PHE cc_start: 0.6031 (OUTLIER) cc_final: 0.5474 (p90) REVERT: E 711 PHE cc_start: 0.6488 (p90) cc_final: 0.6128 (p90) REVERT: E 738 ILE cc_start: 0.6564 (mt) cc_final: 0.6362 (mm) REVERT: F 255 LYS cc_start: 0.8383 (mmtp) cc_final: 0.7871 (mptt) REVERT: F 314 HIS cc_start: 0.6207 (m-70) cc_final: 0.5763 (t70) REVERT: F 321 LYS cc_start: 0.6275 (ttpp) cc_final: 0.5834 (tttm) REVERT: F 373 GLU cc_start: 0.6017 (pt0) cc_final: 0.5079 (pm20) REVERT: G 319 GLN cc_start: 0.5818 (tt0) cc_final: 0.5586 (tt0) REVERT: G 370 SER cc_start: 0.5933 (m) cc_final: 0.5555 (t) REVERT: G 376 ASN cc_start: 0.6490 (m-40) cc_final: 0.6158 (m-40) REVERT: G 417 ASP cc_start: 0.7668 (m-30) cc_final: 0.7429 (m-30) REVERT: G 420 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8461 (p) REVERT: G 520 ASP cc_start: 0.7730 (t0) cc_final: 0.7374 (m-30) REVERT: G 522 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6580 (mm-30) REVERT: G 582 ASP cc_start: 0.7221 (m-30) cc_final: 0.6850 (t0) REVERT: G 583 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6685 (t0) REVERT: H 26 ARG cc_start: 0.4573 (tmm160) cc_final: 0.3538 (ttm110) REVERT: H 40 GLU cc_start: 0.5580 (mm-30) cc_final: 0.5329 (tm-30) REVERT: H 60 TYR cc_start: 0.4242 (m-80) cc_final: 0.3899 (m-80) REVERT: H 65 GLU cc_start: 0.4788 (mt-10) cc_final: 0.4190 (tp30) REVERT: H 78 ASN cc_start: 0.4789 (m-40) cc_final: 0.4443 (m-40) REVERT: H 109 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6491 (tm-30) REVERT: H 143 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6218 (mt-10) REVERT: H 156 MET cc_start: 0.7653 (mmm) cc_final: 0.7343 (mmm) REVERT: H 216 ASP cc_start: 0.5370 (m-30) cc_final: 0.4929 (p0) REVERT: H 233 ASN cc_start: 0.4222 (m-40) cc_final: 0.3920 (t0) REVERT: H 317 GLU cc_start: 0.5031 (tp30) cc_final: 0.4681 (mp0) outliers start: 59 outliers final: 29 residues processed: 337 average time/residue: 1.2072 time to fit residues: 492.8277 Evaluate side-chains 274 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 240 time to evaluate : 2.777 ------------------------------------------------------------------------------- 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 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 594 THR Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 291 ASP 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 G residue 420 SER Chi-restraints excluded: chain G residue 583 ASN Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 266 ASN 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 192 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 288 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 347 optimal weight: 5.9990 chunk 375 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN B 463 ASN B 634 ASN C 225 ASN C 252 GLN C 392 ASN C 627 ASN D 392 ASN D 735 ASN E 368 GLN E 392 ASN E 602 ASN F 640 GLN G 463 ASN G 702 GLN H 127 GLN H 244 ASN H 256 ASN H 384 ASN H 385 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 31177 Z= 0.459 Angle : 0.759 19.335 42251 Z= 0.410 Chirality : 0.054 0.226 4758 Planarity : 0.006 0.064 5493 Dihedral : 5.443 40.886 4207 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.71 % Allowed : 9.82 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 3884 helix: 0.65 (0.21), residues: 595 sheet: 0.51 (0.15), residues: 1184 loop : -1.03 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 632 HIS 0.005 0.002 AHIS A 314 PHE 0.026 0.003 PHE C 711 TYR 0.037 0.003 TYR B 704 ARG 0.010 0.001 ARG A 529 *********************** 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 327 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 238 time to evaluate : 3.634 Fit side-chains REVERT: A 314 HIS cc_start: 0.6744 (m-70) cc_final: 0.5982 (t-90) REVERT: A 319 GLN cc_start: 0.6929 (pt0) cc_final: 0.6328 (pt0) REVERT: A 321 LYS cc_start: 0.5654 (ttpp) cc_final: 0.5141 (ttmt) REVERT: A 371 ASN cc_start: 0.6107 (p0) cc_final: 0.5655 (m-40) REVERT: A 376 ASN cc_start: 0.7140 (m-40) cc_final: 0.6553 (t0) REVERT: A 452 MET cc_start: 0.8916 (ptt) cc_final: 0.8629 (ptt) REVERT: A 499 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6389 (tp30) REVERT: B 313 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 318 ASP cc_start: 0.6337 (m-30) cc_final: 0.6064 (m-30) REVERT: B 376 ASN cc_start: 0.6946 (OUTLIER) cc_final: 0.6726 (t0) REVERT: B 582 ASP cc_start: 0.7836 (m-30) cc_final: 0.7323 (m-30) REVERT: B 705 THR cc_start: 0.6521 (OUTLIER) cc_final: 0.6143 (t) REVERT: C 218 ASP cc_start: 0.6248 (p0) cc_final: 0.5932 (m-30) REVERT: C 313 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7420 (mt-10) REVERT: C 314 HIS cc_start: 0.6840 (m-70) cc_final: 0.6038 (t-90) REVERT: C 381 ILE cc_start: 0.7289 (tp) cc_final: 0.6850 (pt) REVERT: C 536 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7275 (mp-120) REVERT: C 544 GLU cc_start: 0.7664 (tt0) cc_final: 0.7331 (mt-10) REVERT: C 569 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7733 (mp) REVERT: C 582 ASP cc_start: 0.7314 (m-30) cc_final: 0.6970 (m-30) REVERT: C 583 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7514 (m110) REVERT: C 589 LYS cc_start: 0.7719 (ttpp) cc_final: 0.7483 (ptmm) REVERT: C 621 ASN cc_start: 0.6278 (p0) cc_final: 0.5978 (p0) REVERT: C 655 LYS cc_start: 0.5557 (OUTLIER) cc_final: 0.5086 (mmtt) REVERT: C 660 MET cc_start: 0.6580 (tpt) cc_final: 0.6221 (OUTLIER) REVERT: D 318 ASP cc_start: 0.6439 (m-30) cc_final: 0.6232 (m-30) REVERT: D 458 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.6462 (ttt-90) REVERT: D 568 ASP cc_start: 0.6862 (m-30) cc_final: 0.6587 (m-30) REVERT: D 660 MET cc_start: 0.5650 (tpt) cc_final: 0.5073 (tmt) REVERT: E 252 GLN cc_start: 0.7461 (mt0) cc_final: 0.6836 (mm-40) REVERT: E 313 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6880 (mt-10) REVERT: E 373 GLU cc_start: 0.6433 (pt0) cc_final: 0.6218 (pt0) REVERT: E 589 LYS cc_start: 0.7644 (ttpp) cc_final: 0.7348 (tttm) REVERT: E 660 MET cc_start: 0.6166 (tpt) cc_final: 0.5861 (tpt) REVERT: E 707 PHE cc_start: 0.5794 (OUTLIER) cc_final: 0.4003 (p90) REVERT: E 738 ILE cc_start: 0.6610 (mt) cc_final: 0.6338 (mp) REVERT: F 218 ASP cc_start: 0.6772 (p0) cc_final: 0.6536 (p0) REVERT: F 314 HIS cc_start: 0.6360 (m-70) cc_final: 0.5992 (t70) REVERT: F 321 LYS cc_start: 0.6405 (ttpp) cc_final: 0.6145 (tttm) REVERT: F 373 GLU cc_start: 0.6327 (pt0) cc_final: 0.5990 (pt0) REVERT: F 426 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7486 (mm-30) REVERT: F 583 ASN cc_start: 0.7696 (m110) cc_final: 0.7184 (t0) REVERT: F 706 LYS cc_start: 0.5711 (mtmt) cc_final: 0.5389 (mtmt) REVERT: G 417 ASP cc_start: 0.7692 (m-30) cc_final: 0.7469 (m-30) REVERT: G 582 ASP cc_start: 0.7480 (m-30) cc_final: 0.7251 (t0) REVERT: H 26 ARG cc_start: 0.4106 (tmm160) cc_final: 0.3132 (ttm110) REVERT: H 65 GLU cc_start: 0.4510 (mt-10) cc_final: 0.4049 (tp30) REVERT: H 77 ARG cc_start: 0.5281 (ttp80) cc_final: 0.4893 (ttp80) REVERT: H 78 ASN cc_start: 0.4424 (m-40) cc_final: 0.3975 (m-40) REVERT: H 109 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6698 (tm-30) REVERT: H 118 LYS cc_start: 0.6645 (OUTLIER) cc_final: 0.6055 (mmpt) REVERT: H 143 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6179 (mt-10) REVERT: H 180 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: H 216 ASP cc_start: 0.5637 (m-30) cc_final: 0.4868 (p0) REVERT: H 247 MET cc_start: 0.3846 (tmm) cc_final: 0.2640 (tpp) REVERT: H 372 ILE cc_start: 0.2457 (OUTLIER) cc_final: 0.2241 (pp) outliers start: 89 outliers final: 54 residues processed: 306 average time/residue: 1.1949 time to fit residues: 444.6412 Evaluate side-chains 266 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 203 time to evaluate : 3.715 ------------------------------------------------------------------------------- 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 568 ASP 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 376 ASN Chi-restraints excluded: chain B residue 568 ASP 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 317 THR Chi-restraints excluded: chain C residue 377 THR 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 C residue 583 ASN Chi-restraints excluded: chain C residue 655 LYS 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 377 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 E residue 264 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 594 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 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 516 SER 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 636 ASN Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain H residue 50 SER 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 180 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 324 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 165 optimal weight: 0.0020 chunk 233 optimal weight: 0.7980 chunk 348 optimal weight: 0.9980 chunk 369 optimal weight: 0.2980 chunk 182 optimal weight: 0.9980 chunk 330 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 368 GLN A 463 ASN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 463 ASN C 252 GLN C 463 ASN C 627 ASN F 368 GLN F 463 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 31177 Z= 0.145 Angle : 0.518 15.684 42251 Z= 0.278 Chirality : 0.044 0.162 4758 Planarity : 0.004 0.060 5493 Dihedral : 4.747 41.376 4207 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.96 % Allowed : 11.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3884 helix: 1.24 (0.22), residues: 590 sheet: 0.76 (0.15), residues: 1202 loop : -0.91 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 375 HIS 0.003 0.001 HIS H 157 PHE 0.020 0.001 PHE C 711 TYR 0.020 0.001 TYR B 704 ARG 0.006 0.000 ARG H 77 *********************** 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 303 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 240 time to evaluate : 3.730 Fit side-chains REVERT: A 269 ASP cc_start: 0.8049 (p0) cc_final: 0.7696 (p0) REVERT: A 314 HIS cc_start: 0.6711 (m-70) cc_final: 0.6010 (t-90) REVERT: A 319 GLN cc_start: 0.6629 (pt0) cc_final: 0.6085 (pt0) REVERT: A 321 LYS cc_start: 0.5558 (ttpp) cc_final: 0.5120 (ttmt) REVERT: A 371 ASN cc_start: 0.5924 (p0) cc_final: 0.5639 (m-40) REVERT: A 376 ASN cc_start: 0.7178 (m-40) cc_final: 0.6525 (t0) REVERT: A 452 MET cc_start: 0.8909 (ptt) cc_final: 0.8651 (ptt) REVERT: A 499 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6267 (tp30) REVERT: A 544 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: B 263 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7318 (mm-30) REVERT: B 313 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7451 (mt-10) REVERT: B 582 ASP cc_start: 0.7786 (m-30) cc_final: 0.7268 (m-30) REVERT: C 218 ASP cc_start: 0.6286 (OUTLIER) cc_final: 0.5922 (m-30) REVERT: C 314 HIS cc_start: 0.6840 (m-70) cc_final: 0.6096 (t-90) REVERT: C 381 ILE cc_start: 0.7314 (tp) cc_final: 0.6868 (pt) REVERT: C 536 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7183 (mp-120) REVERT: C 544 GLU cc_start: 0.7648 (tt0) cc_final: 0.7303 (mt-10) REVERT: C 569 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7785 (mp) REVERT: C 582 ASP cc_start: 0.7396 (m-30) cc_final: 0.7063 (m-30) REVERT: C 589 LYS cc_start: 0.7800 (ttpp) cc_final: 0.7123 (ptpp) REVERT: C 660 MET cc_start: 0.6261 (tpt) cc_final: 0.5980 (mmt) REVERT: D 317 THR cc_start: 0.7456 (m) cc_final: 0.7056 (p) REVERT: D 318 ASP cc_start: 0.6192 (m-30) cc_final: 0.5910 (m-30) REVERT: D 376 ASN cc_start: 0.7237 (m-40) cc_final: 0.6969 (m-40) REVERT: D 382 ASN cc_start: 0.8041 (t0) cc_final: 0.7744 (t0) REVERT: D 452 MET cc_start: 0.8582 (ptt) cc_final: 0.8358 (ptt) REVERT: D 458 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.6475 (ttt-90) REVERT: D 568 ASP cc_start: 0.6902 (m-30) cc_final: 0.6646 (m-30) REVERT: D 660 MET cc_start: 0.5870 (tpt) cc_final: 0.5312 (tmt) REVERT: E 251 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7047 (mm-30) REVERT: E 252 GLN cc_start: 0.7510 (mt0) cc_final: 0.6944 (mm-40) REVERT: E 313 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6790 (mt-10) REVERT: E 319 GLN cc_start: 0.6602 (mt0) cc_final: 0.5855 (mt0) REVERT: E 321 LYS cc_start: 0.6353 (ttpt) cc_final: 0.5625 (tttt) REVERT: E 589 LYS cc_start: 0.7590 (ttpp) cc_final: 0.7288 (tttm) REVERT: E 660 MET cc_start: 0.6383 (tpt) cc_final: 0.6095 (tpt) REVERT: E 707 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.4408 (p90) REVERT: E 738 ILE cc_start: 0.6328 (mt) cc_final: 0.6097 (mp) REVERT: F 314 HIS cc_start: 0.6332 (m-70) cc_final: 0.5992 (t70) REVERT: F 373 GLU cc_start: 0.6187 (pt0) cc_final: 0.5860 (pt0) REVERT: F 426 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7464 (mm-30) REVERT: F 583 ASN cc_start: 0.7766 (m110) cc_final: 0.7132 (t0) REVERT: F 704 TYR cc_start: 0.5846 (m-80) cc_final: 0.5581 (m-80) REVERT: F 722 GLU cc_start: 0.5996 (mm-30) cc_final: 0.5709 (mm-30) REVERT: G 426 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: G 582 ASP cc_start: 0.7455 (m-30) cc_final: 0.7170 (t0) REVERT: G 583 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7253 (m110) REVERT: G 667 LYS cc_start: 0.4827 (mtpp) cc_final: 0.4438 (mmmt) REVERT: H 26 ARG cc_start: 0.4008 (tmm160) cc_final: 0.2989 (ttm110) REVERT: H 40 GLU cc_start: 0.5466 (mm-30) cc_final: 0.5229 (mm-30) REVERT: H 60 TYR cc_start: 0.4348 (m-80) cc_final: 0.2938 (t80) REVERT: H 65 GLU cc_start: 0.4585 (mt-10) cc_final: 0.4120 (tp30) REVERT: H 78 ASN cc_start: 0.4619 (m-40) cc_final: 0.4217 (m-40) REVERT: H 109 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6678 (tm-30) REVERT: H 143 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6081 (mt-10) REVERT: H 180 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6866 (tt0) REVERT: H 216 ASP cc_start: 0.5595 (m-30) cc_final: 0.4736 (p0) REVERT: H 247 MET cc_start: 0.3755 (tmm) cc_final: 0.2612 (tpp) REVERT: H 372 ILE cc_start: 0.2296 (OUTLIER) cc_final: 0.2073 (pp) outliers start: 63 outliers final: 32 residues processed: 284 average time/residue: 1.2036 time to fit residues: 414.9867 Evaluate side-chains 260 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 3.821 ------------------------------------------------------------------------------- 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 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 C residue 218 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 380 SER 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 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 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 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 465 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 569 ILE 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 G residue 594 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 217 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 274 optimal weight: 0.5980 chunk 152 optimal weight: 0.0270 chunk 315 optimal weight: 0.6980 chunk 255 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 463 ASN C 252 GLN C 463 ASN C 627 ASN D 735 ASN E 627 ASN E 634 ASN E 702 GLN H 277 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31177 Z= 0.221 Angle : 0.569 16.650 42251 Z= 0.306 Chirality : 0.046 0.167 4758 Planarity : 0.004 0.060 5493 Dihedral : 4.905 40.321 4207 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.57 % Allowed : 12.21 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3884 helix: 1.14 (0.22), residues: 596 sheet: 0.74 (0.16), residues: 1199 loop : -0.99 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 375 HIS 0.003 0.001 AHIS A 314 PHE 0.017 0.002 PHE C 711 TYR 0.023 0.002 TYR H 246 ARG 0.004 0.001 ARG H 77 *********************** 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 300 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 216 time to evaluate : 3.858 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.8132 (p0) cc_final: 0.7769 (p0) REVERT: A 314 HIS cc_start: 0.6662 (m-70) cc_final: 0.6022 (t-90) REVERT: A 319 GLN cc_start: 0.6661 (pt0) cc_final: 0.6156 (tt0) REVERT: A 321 LYS cc_start: 0.5720 (ttpp) cc_final: 0.5139 (mtmt) REVERT: A 376 ASN cc_start: 0.7157 (m-40) cc_final: 0.6471 (t0) REVERT: A 452 MET cc_start: 0.8907 (ptt) cc_final: 0.8657 (ptt) REVERT: A 499 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6336 (tp30) REVERT: A 544 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: B 313 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7552 (mt-10) REVERT: B 582 ASP cc_start: 0.7797 (m-30) cc_final: 0.7288 (m-30) REVERT: C 218 ASP cc_start: 0.6181 (OUTLIER) cc_final: 0.5864 (m-30) REVERT: C 314 HIS cc_start: 0.6859 (m-70) cc_final: 0.6108 (t-90) REVERT: C 381 ILE cc_start: 0.7337 (tp) cc_final: 0.6876 (pt) REVERT: C 495 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7214 (tp40) REVERT: C 536 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7247 (mp-120) REVERT: C 544 GLU cc_start: 0.7716 (tt0) cc_final: 0.7367 (mt-10) REVERT: C 582 ASP cc_start: 0.7402 (m-30) cc_final: 0.7068 (m-30) REVERT: C 655 LYS cc_start: 0.5483 (OUTLIER) cc_final: 0.5151 (mmtt) REVERT: C 710 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6326 (mt-10) REVERT: D 314 HIS cc_start: 0.6554 (m-70) cc_final: 0.5659 (t70) REVERT: D 317 THR cc_start: 0.7457 (m) cc_final: 0.7027 (p) REVERT: D 318 ASP cc_start: 0.6240 (m-30) cc_final: 0.5898 (m-30) REVERT: D 376 ASN cc_start: 0.7230 (m-40) cc_final: 0.6958 (m-40) REVERT: D 458 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.6535 (ttt-90) REVERT: D 568 ASP cc_start: 0.7019 (m-30) cc_final: 0.6749 (m-30) REVERT: D 660 MET cc_start: 0.5897 (tpt) cc_final: 0.5370 (tmt) REVERT: E 252 GLN cc_start: 0.7460 (mt0) cc_final: 0.6910 (mm-40) REVERT: E 313 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6808 (mt-10) REVERT: E 319 GLN cc_start: 0.6636 (mt0) cc_final: 0.5903 (mt0) REVERT: E 321 LYS cc_start: 0.6372 (ttpt) cc_final: 0.5637 (tttt) REVERT: E 376 ASN cc_start: 0.6900 (m-40) cc_final: 0.6441 (t0) REVERT: E 589 LYS cc_start: 0.7604 (ttpp) cc_final: 0.7298 (tttm) REVERT: E 606 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7078 (mt-10) REVERT: E 660 MET cc_start: 0.6323 (tpt) cc_final: 0.6002 (tpt) REVERT: E 738 ILE cc_start: 0.6314 (mt) cc_final: 0.6113 (mp) REVERT: F 218 ASP cc_start: 0.6506 (p0) cc_final: 0.6169 (p0) REVERT: F 314 HIS cc_start: 0.6318 (m-70) cc_final: 0.5960 (t70) REVERT: F 321 LYS cc_start: 0.6260 (tttm) cc_final: 0.5960 (ttpp) REVERT: F 373 GLU cc_start: 0.6177 (pt0) cc_final: 0.5856 (pt0) REVERT: F 426 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7459 (mm-30) REVERT: F 582 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6691 (t70) REVERT: F 583 ASN cc_start: 0.7758 (m110) cc_final: 0.7166 (t0) REVERT: F 706 LYS cc_start: 0.5573 (mtmt) cc_final: 0.5258 (mtmt) REVERT: F 722 GLU cc_start: 0.5895 (mm-30) cc_final: 0.5555 (mm-30) REVERT: G 291 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.7688 (p0) REVERT: G 370 SER cc_start: 0.6044 (m) cc_final: 0.5606 (t) REVERT: G 426 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: G 582 ASP cc_start: 0.7565 (m-30) cc_final: 0.7283 (t0) REVERT: G 583 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7324 (m110) REVERT: G 667 LYS cc_start: 0.4897 (mtpp) cc_final: 0.4512 (mmmt) REVERT: H 65 GLU cc_start: 0.4642 (mt-10) cc_final: 0.4131 (tp30) REVERT: H 77 ARG cc_start: 0.5343 (ttp80) cc_final: 0.4998 (ttp80) REVERT: H 78 ASN cc_start: 0.4314 (m-40) cc_final: 0.3846 (m-40) REVERT: H 109 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6628 (tm-30) REVERT: H 143 GLU cc_start: 0.6386 (mt-10) cc_final: 0.6024 (mt-10) REVERT: H 180 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6732 (tt0) REVERT: H 216 ASP cc_start: 0.5614 (m-30) cc_final: 0.4737 (p0) REVERT: H 247 MET cc_start: 0.3779 (tmm) cc_final: 0.2681 (tpp) REVERT: H 372 ILE cc_start: 0.2556 (OUTLIER) cc_final: 0.2315 (pp) outliers start: 84 outliers final: 46 residues processed: 282 average time/residue: 1.2081 time to fit residues: 415.0395 Evaluate side-chains 267 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 209 time to evaluate : 3.393 ------------------------------------------------------------------------------- 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 568 ASP Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP 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 542 THR 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 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 594 THR Chi-restraints excluded: chain E residue 606 GLU Chi-restraints excluded: chain E residue 661 SER 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 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 582 ASP Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 583 ASN Chi-restraints excluded: chain G residue 594 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 132 LYS 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 266 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 369 optimal weight: 2.9990 chunk 306 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 0.0980 chunk 194 optimal weight: 8.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 463 ASN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 463 ASN C 627 ASN D 495 GLN B E 627 ASN H 277 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31177 Z= 0.266 Angle : 0.613 17.405 42251 Z= 0.330 Chirality : 0.047 0.170 4758 Planarity : 0.005 0.063 5493 Dihedral : 5.111 41.619 4207 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.66 % Allowed : 12.67 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 3884 helix: 0.99 (0.22), residues: 596 sheet: 0.65 (0.15), residues: 1195 loop : -1.07 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 375 HIS 0.003 0.001 AHIS A 314 PHE 0.016 0.002 PHE A 711 TYR 0.028 0.002 TYR B 704 ARG 0.005 0.001 ARG A 529 *********************** 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 298 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 210 time to evaluate : 3.494 Fit side-chains REVERT: A 269 ASP cc_start: 0.8210 (p0) cc_final: 0.7881 (p0) REVERT: A 314 HIS cc_start: 0.6597 (m-70) cc_final: 0.5943 (t-90) REVERT: A 319 GLN cc_start: 0.6779 (pt0) cc_final: 0.6269 (tt0) REVERT: A 321 LYS cc_start: 0.5761 (ttpp) cc_final: 0.5156 (mtmt) REVERT: A 376 ASN cc_start: 0.7155 (m-40) cc_final: 0.6470 (t0) REVERT: A 452 MET cc_start: 0.8917 (ptt) cc_final: 0.8660 (ptt) REVERT: A 499 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6339 (tp30) REVERT: A 544 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: B 313 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7577 (mt-10) REVERT: B 371 ASN cc_start: 0.6258 (m-40) cc_final: 0.6051 (m-40) REVERT: B 376 ASN cc_start: 0.7009 (OUTLIER) cc_final: 0.6760 (t0) REVERT: B 582 ASP cc_start: 0.7843 (m-30) cc_final: 0.7336 (m-30) REVERT: B 705 THR cc_start: 0.6583 (OUTLIER) cc_final: 0.6177 (t) REVERT: C 218 ASP cc_start: 0.6208 (OUTLIER) cc_final: 0.5843 (m-30) REVERT: C 314 HIS cc_start: 0.6827 (m-70) cc_final: 0.6024 (t-90) REVERT: C 381 ILE cc_start: 0.7339 (tp) cc_final: 0.6881 (pt) REVERT: C 495 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7217 (tp40) REVERT: C 536 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7223 (mp-120) REVERT: C 544 GLU cc_start: 0.7707 (tt0) cc_final: 0.7378 (mt-10) REVERT: C 582 ASP cc_start: 0.7405 (m-30) cc_final: 0.7054 (m-30) REVERT: C 583 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7311 (m110) REVERT: C 655 LYS cc_start: 0.5480 (OUTLIER) cc_final: 0.5159 (mmtt) REVERT: C 710 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6371 (mt-10) REVERT: D 314 HIS cc_start: 0.6469 (m-70) cc_final: 0.5645 (t70) REVERT: D 318 ASP cc_start: 0.6337 (m-30) cc_final: 0.6065 (m-30) REVERT: D 376 ASN cc_start: 0.7284 (m-40) cc_final: 0.6983 (m-40) REVERT: D 458 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6550 (ttt-90) REVERT: D 568 ASP cc_start: 0.7100 (m-30) cc_final: 0.6828 (m-30) REVERT: D 660 MET cc_start: 0.5898 (tpt) cc_final: 0.5325 (tmt) REVERT: E 252 GLN cc_start: 0.7325 (mt0) cc_final: 0.6915 (mm-40) REVERT: E 321 LYS cc_start: 0.6290 (ttpt) cc_final: 0.5615 (tttt) REVERT: E 589 LYS cc_start: 0.7653 (ttpp) cc_final: 0.7407 (ttpt) REVERT: E 606 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: E 660 MET cc_start: 0.6374 (tpt) cc_final: 0.6094 (tpt) REVERT: F 218 ASP cc_start: 0.6447 (p0) cc_final: 0.6122 (p0) REVERT: F 314 HIS cc_start: 0.6332 (m-70) cc_final: 0.6035 (t70) REVERT: F 321 LYS cc_start: 0.6308 (tttm) cc_final: 0.5991 (ttpp) REVERT: F 426 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7490 (mm-30) REVERT: F 582 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6734 (t70) REVERT: F 583 ASN cc_start: 0.7754 (m110) cc_final: 0.7149 (t0) REVERT: F 706 LYS cc_start: 0.5692 (mtmt) cc_final: 0.5392 (mtmt) REVERT: F 707 PHE cc_start: 0.5784 (OUTLIER) cc_final: 0.3563 (p90) REVERT: F 722 GLU cc_start: 0.5932 (mm-30) cc_final: 0.5510 (mm-30) REVERT: G 370 SER cc_start: 0.6062 (m) cc_final: 0.5632 (t) REVERT: G 426 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: G 583 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7318 (m110) REVERT: G 667 LYS cc_start: 0.4921 (mtpp) cc_final: 0.4562 (mmmt) REVERT: H 65 GLU cc_start: 0.4633 (mt-10) cc_final: 0.4122 (tp30) REVERT: H 77 ARG cc_start: 0.5380 (ttp80) cc_final: 0.5016 (ttp80) REVERT: H 78 ASN cc_start: 0.4185 (m-40) cc_final: 0.3844 (m-40) REVERT: H 109 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6600 (tm-30) REVERT: H 143 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6050 (mt-10) REVERT: H 156 MET cc_start: 0.7695 (mmm) cc_final: 0.7106 (mmm) REVERT: H 180 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6759 (tt0) REVERT: H 216 ASP cc_start: 0.5514 (m-30) cc_final: 0.4773 (p0) REVERT: H 247 MET cc_start: 0.4077 (tmm) cc_final: 0.2972 (tpp) REVERT: H 372 ILE cc_start: 0.2602 (OUTLIER) cc_final: 0.2343 (pp) outliers start: 88 outliers final: 54 residues processed: 280 average time/residue: 1.2287 time to fit residues: 422.5590 Evaluate side-chains 269 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 200 time to evaluate : 3.726 ------------------------------------------------------------------------------- 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 544 GLU Chi-restraints excluded: chain A residue 568 ASP 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 376 ASN Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 377 THR 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 542 THR Chi-restraints excluded: chain C residue 583 ASN 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 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 480 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 606 GLU Chi-restraints excluded: chain E residue 661 SER 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 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 582 ASP Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 710 GLU Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 583 ASN Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 132 LYS 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 339 THR Chi-restraints excluded: chain H residue 372 ILE Chi-restraints excluded: chain H residue 387 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 368 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 319 GLN B 463 ASN B 636 ASN C 627 ASN E 627 ASN H 277 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31177 Z= 0.230 Angle : 0.577 16.786 42251 Z= 0.310 Chirality : 0.046 0.162 4758 Planarity : 0.004 0.061 5493 Dihedral : 4.993 40.782 4207 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.68 % Allowed : 13.16 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 3884 helix: 1.08 (0.22), residues: 596 sheet: 0.67 (0.15), residues: 1199 loop : -1.04 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 375 HIS 0.002 0.001 HIS H 199 PHE 0.028 0.002 PHE C 711 TYR 0.025 0.002 TYR B 704 ARG 0.004 0.001 ARG F 232 *********************** 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 299 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 210 time to evaluate : 4.011 Fit side-chains REVERT: A 269 ASP cc_start: 0.8157 (p0) cc_final: 0.7803 (p0) REVERT: A 314 HIS cc_start: 0.6588 (m-70) cc_final: 0.5949 (t-90) REVERT: A 319 GLN cc_start: 0.6559 (pt0) cc_final: 0.6142 (tt0) REVERT: A 321 LYS cc_start: 0.5777 (ttpp) cc_final: 0.5129 (mtmt) REVERT: A 376 ASN cc_start: 0.7111 (m-40) cc_final: 0.6431 (t0) REVERT: A 452 MET cc_start: 0.8914 (ptt) cc_final: 0.8642 (ptt) REVERT: A 499 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6301 (tp30) REVERT: A 544 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: B 313 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 318 ASP cc_start: 0.6082 (m-30) cc_final: 0.5621 (m-30) REVERT: B 371 ASN cc_start: 0.6295 (m-40) cc_final: 0.6074 (m-40) REVERT: B 582 ASP cc_start: 0.7831 (m-30) cc_final: 0.7315 (m-30) REVERT: B 701 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5906 (mp0) REVERT: B 705 THR cc_start: 0.6578 (OUTLIER) cc_final: 0.6096 (t) REVERT: C 218 ASP cc_start: 0.6215 (OUTLIER) cc_final: 0.5879 (m-30) REVERT: C 314 HIS cc_start: 0.6855 (m-70) cc_final: 0.6096 (t-90) REVERT: C 381 ILE cc_start: 0.7343 (tp) cc_final: 0.6879 (pt) REVERT: C 495 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7221 (tp40) REVERT: C 536 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7166 (mp-120) REVERT: C 544 GLU cc_start: 0.7680 (tt0) cc_final: 0.7349 (mt-10) REVERT: C 582 ASP cc_start: 0.7400 (m-30) cc_final: 0.7045 (m-30) REVERT: C 583 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7313 (m110) REVERT: C 655 LYS cc_start: 0.5484 (OUTLIER) cc_final: 0.5189 (mmtt) REVERT: C 670 VAL cc_start: 0.7536 (t) cc_final: 0.7206 (p) REVERT: C 710 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6426 (mt-10) REVERT: D 314 HIS cc_start: 0.6463 (m-70) cc_final: 0.5614 (t70) REVERT: D 318 ASP cc_start: 0.6298 (m-30) cc_final: 0.6040 (m-30) REVERT: D 376 ASN cc_start: 0.7253 (m-40) cc_final: 0.6976 (m-40) REVERT: D 382 ASN cc_start: 0.8063 (t0) cc_final: 0.7749 (t0) REVERT: D 452 MET cc_start: 0.8596 (ptt) cc_final: 0.8310 (ptt) REVERT: D 458 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.6662 (ttt-90) REVERT: D 568 ASP cc_start: 0.7096 (m-30) cc_final: 0.6808 (m-30) REVERT: D 660 MET cc_start: 0.5921 (tpt) cc_final: 0.5581 (tpt) REVERT: E 252 GLN cc_start: 0.7282 (mt0) cc_final: 0.6942 (mm110) REVERT: E 321 LYS cc_start: 0.6270 (ttpt) cc_final: 0.5593 (tttt) REVERT: E 589 LYS cc_start: 0.7608 (ttpp) cc_final: 0.7262 (tttm) REVERT: E 660 MET cc_start: 0.6368 (tpt) cc_final: 0.6037 (tpt) REVERT: F 218 ASP cc_start: 0.6440 (p0) cc_final: 0.6092 (p0) REVERT: F 314 HIS cc_start: 0.6327 (m-70) cc_final: 0.6027 (t70) REVERT: F 321 LYS cc_start: 0.6282 (tttm) cc_final: 0.5977 (ttpp) REVERT: F 426 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7466 (mm-30) REVERT: F 582 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6679 (t70) REVERT: F 583 ASN cc_start: 0.7754 (m110) cc_final: 0.7133 (t0) REVERT: F 706 LYS cc_start: 0.5868 (mtmt) cc_final: 0.5603 (mtmt) REVERT: F 722 GLU cc_start: 0.5902 (mm-30) cc_final: 0.5512 (mm-30) REVERT: G 291 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.7727 (p0) REVERT: G 426 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: G 583 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.6915 (t0) REVERT: G 667 LYS cc_start: 0.4910 (mtpp) cc_final: 0.4381 (mmpt) REVERT: H 51 LYS cc_start: 0.4727 (OUTLIER) cc_final: 0.4359 (mtpt) REVERT: H 60 TYR cc_start: 0.4181 (m-80) cc_final: 0.3128 (t80) REVERT: H 65 GLU cc_start: 0.4713 (mt-10) cc_final: 0.4058 (tp30) REVERT: H 77 ARG cc_start: 0.5373 (ttp80) cc_final: 0.5060 (tmm-80) REVERT: H 109 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6596 (tm-30) REVERT: H 143 GLU cc_start: 0.6421 (mt-10) cc_final: 0.6016 (mt-10) REVERT: H 156 MET cc_start: 0.7603 (mmm) cc_final: 0.7026 (mmm) REVERT: H 180 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6794 (tt0) REVERT: H 216 ASP cc_start: 0.5606 (m-30) cc_final: 0.4863 (p0) REVERT: H 247 MET cc_start: 0.4110 (tmm) cc_final: 0.2888 (tpp) REVERT: H 355 VAL cc_start: 0.4518 (OUTLIER) cc_final: 0.4136 (m) REVERT: H 372 ILE cc_start: 0.2402 (OUTLIER) cc_final: 0.2133 (pp) outliers start: 89 outliers final: 57 residues processed: 280 average time/residue: 1.1713 time to fit residues: 403.6402 Evaluate side-chains 276 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 203 time to evaluate : 3.501 ------------------------------------------------------------------------------- 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 544 GLU Chi-restraints excluded: chain A residue 568 ASP 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 701 GLU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 377 THR 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 542 THR Chi-restraints excluded: chain C residue 583 ASN 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 377 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 480 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 661 SER 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 489 THR 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 582 ASP Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 535 LEU Chi-restraints excluded: chain G residue 583 ASN Chi-restraints excluded: chain H residue 50 SER 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 177 THR Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 355 VAL 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 227 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 289 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 463 ASN C 627 ASN E 602 ASN E 627 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31177 Z= 0.184 Angle : 0.547 16.044 42251 Z= 0.293 Chirality : 0.045 0.163 4758 Planarity : 0.004 0.060 5493 Dihedral : 4.853 41.279 4207 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.48 % Allowed : 13.28 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3884 helix: 1.18 (0.22), residues: 595 sheet: 0.72 (0.16), residues: 1195 loop : -1.00 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 375 HIS 0.002 0.001 HIS H 199 PHE 0.025 0.002 PHE C 711 TYR 0.022 0.001 TYR B 704 ARG 0.003 0.000 ARG H 77 *********************** 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 301 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 219 time to evaluate : 3.680 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.8066 (p0) cc_final: 0.7695 (p0) REVERT: A 314 HIS cc_start: 0.6589 (m-70) cc_final: 0.5966 (t-90) REVERT: A 319 GLN cc_start: 0.6493 (pt0) cc_final: 0.6050 (tt0) REVERT: A 321 LYS cc_start: 0.5764 (ttpp) cc_final: 0.5139 (mtmt) REVERT: A 376 ASN cc_start: 0.7196 (m-40) cc_final: 0.6444 (t0) REVERT: A 452 MET cc_start: 0.8910 (ptt) cc_final: 0.8658 (ptt) REVERT: A 499 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6295 (tp30) REVERT: A 544 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: B 313 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7487 (mt-10) REVERT: B 318 ASP cc_start: 0.6125 (m-30) cc_final: 0.5639 (m-30) REVERT: B 371 ASN cc_start: 0.6230 (m-40) cc_final: 0.6010 (m-40) REVERT: B 376 ASN cc_start: 0.6818 (OUTLIER) cc_final: 0.6578 (t0) REVERT: B 582 ASP cc_start: 0.7796 (m-30) cc_final: 0.7281 (m-30) REVERT: B 701 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5915 (mp0) REVERT: B 705 THR cc_start: 0.6536 (OUTLIER) cc_final: 0.6046 (t) REVERT: C 218 ASP cc_start: 0.6151 (OUTLIER) cc_final: 0.5828 (m-30) REVERT: C 252 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.6241 (mp10) REVERT: C 314 HIS cc_start: 0.6827 (m-70) cc_final: 0.6060 (t-90) REVERT: C 318 ASP cc_start: 0.6248 (m-30) cc_final: 0.5778 (t70) REVERT: C 370 SER cc_start: 0.5662 (m) cc_final: 0.5438 (p) REVERT: C 381 ILE cc_start: 0.7341 (tp) cc_final: 0.6893 (pt) REVERT: C 495 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7202 (tp40) REVERT: C 536 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7178 (mp-120) REVERT: C 544 GLU cc_start: 0.7717 (tt0) cc_final: 0.7390 (mt-10) REVERT: C 582 ASP cc_start: 0.7416 (m-30) cc_final: 0.7070 (m-30) REVERT: C 583 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7346 (m110) REVERT: C 655 LYS cc_start: 0.5471 (OUTLIER) cc_final: 0.5140 (mmtt) REVERT: C 670 VAL cc_start: 0.7484 (t) cc_final: 0.7146 (p) REVERT: C 710 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6327 (mt-10) REVERT: D 314 HIS cc_start: 0.6440 (m-70) cc_final: 0.5606 (t70) REVERT: D 318 ASP cc_start: 0.6212 (m-30) cc_final: 0.5935 (m-30) REVERT: D 376 ASN cc_start: 0.7243 (m-40) cc_final: 0.7021 (m-40) REVERT: D 382 ASN cc_start: 0.8066 (t0) cc_final: 0.7779 (t0) REVERT: D 452 MET cc_start: 0.8595 (ptt) cc_final: 0.8324 (ptt) REVERT: D 458 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6509 (ttt-90) REVERT: D 568 ASP cc_start: 0.7096 (m-30) cc_final: 0.6810 (m-30) REVERT: D 660 MET cc_start: 0.5931 (tpt) cc_final: 0.5115 (tpp) REVERT: E 252 GLN cc_start: 0.7146 (mt0) cc_final: 0.6869 (mm-40) REVERT: E 313 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6773 (mt-10) REVERT: E 321 LYS cc_start: 0.6387 (ttpt) cc_final: 0.5661 (tttt) REVERT: E 589 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7261 (tttm) REVERT: E 606 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: E 660 MET cc_start: 0.6319 (tpt) cc_final: 0.5988 (tpt) REVERT: F 314 HIS cc_start: 0.6315 (m-70) cc_final: 0.6028 (t70) REVERT: F 321 LYS cc_start: 0.6258 (tttm) cc_final: 0.5963 (ttpp) REVERT: F 373 GLU cc_start: 0.6241 (pt0) cc_final: 0.5951 (pt0) REVERT: F 426 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7458 (mm-30) REVERT: F 582 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6652 (t70) REVERT: F 583 ASN cc_start: 0.7745 (m110) cc_final: 0.7117 (t0) REVERT: F 706 LYS cc_start: 0.5820 (mtmt) cc_final: 0.5552 (mtmt) REVERT: F 707 PHE cc_start: 0.5651 (OUTLIER) cc_final: 0.3461 (p90) REVERT: F 722 GLU cc_start: 0.5664 (mm-30) cc_final: 0.5275 (mm-30) REVERT: G 291 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.7698 (p0) REVERT: G 426 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: G 583 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.6928 (t0) REVERT: G 667 LYS cc_start: 0.4893 (mtpp) cc_final: 0.4370 (mmpt) REVERT: H 30 LYS cc_start: 0.4896 (mmmt) cc_final: 0.4629 (mtpt) REVERT: H 51 LYS cc_start: 0.4841 (OUTLIER) cc_final: 0.4472 (mtpt) REVERT: H 65 GLU cc_start: 0.4750 (mt-10) cc_final: 0.4105 (mm-30) REVERT: H 77 ARG cc_start: 0.5318 (ttp80) cc_final: 0.5029 (tmm-80) REVERT: H 109 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6601 (tm-30) REVERT: H 143 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6013 (mt-10) REVERT: H 156 MET cc_start: 0.7594 (mmm) cc_final: 0.7158 (mmm) REVERT: H 180 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6798 (tt0) REVERT: H 216 ASP cc_start: 0.5555 (m-30) cc_final: 0.4830 (p0) REVERT: H 247 MET cc_start: 0.4137 (tmm) cc_final: 0.2887 (tpp) REVERT: H 352 ARG cc_start: 0.3033 (mtt90) cc_final: 0.2778 (mtt90) REVERT: H 355 VAL cc_start: 0.4533 (OUTLIER) cc_final: 0.4162 (m) REVERT: H 372 ILE cc_start: 0.2377 (OUTLIER) cc_final: 0.2129 (pp) outliers start: 82 outliers final: 55 residues processed: 282 average time/residue: 1.1634 time to fit residues: 402.6964 Evaluate side-chains 284 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 209 time to evaluate : 3.855 ------------------------------------------------------------------------------- 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 544 GLU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 218 ASP 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 319 GLN Chi-restraints excluded: chain C residue 322 THR 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 542 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 654 THR 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 377 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 264 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 318 ASP 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 661 SER 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 569 ILE Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 636 ASN 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 291 ASP Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 583 ASN Chi-restraints excluded: chain H residue 50 SER 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 177 THR Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 372 ILE 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 334 optimal weight: 2.9990 chunk 352 optimal weight: 4.9990 chunk 321 optimal weight: 2.9990 chunk 343 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 269 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 chunk 324 optimal weight: 0.6980 chunk 341 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 463 ASN C 627 ASN H 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31177 Z= 0.298 Angle : 0.631 17.892 42251 Z= 0.340 Chirality : 0.048 0.165 4758 Planarity : 0.005 0.061 5493 Dihedral : 5.168 40.466 4207 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.71 % Allowed : 13.31 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 3884 helix: 0.93 (0.22), residues: 595 sheet: 0.62 (0.15), residues: 1196 loop : -1.09 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 375 HIS 0.003 0.001 AHIS A 314 PHE 0.025 0.002 PHE C 711 TYR 0.028 0.002 TYR B 704 ARG 0.005 0.001 ARG F 232 *********************** 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 300 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 210 time to evaluate : 3.679 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.8236 (p0) cc_final: 0.7907 (p0) REVERT: A 314 HIS cc_start: 0.6626 (m-70) cc_final: 0.5964 (t-90) REVERT: A 319 GLN cc_start: 0.6668 (pt0) cc_final: 0.6191 (tt0) REVERT: A 321 LYS cc_start: 0.5704 (ttpp) cc_final: 0.5090 (mtmt) REVERT: A 376 ASN cc_start: 0.7177 (m-40) cc_final: 0.6476 (t0) REVERT: A 452 MET cc_start: 0.8917 (ptt) cc_final: 0.8661 (ptt) REVERT: A 499 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6364 (tp30) REVERT: A 544 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: B 313 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7575 (mt-10) REVERT: B 318 ASP cc_start: 0.6092 (m-30) cc_final: 0.5655 (m-30) REVERT: B 371 ASN cc_start: 0.6379 (m-40) cc_final: 0.6175 (m-40) REVERT: B 376 ASN cc_start: 0.6877 (OUTLIER) cc_final: 0.6626 (t0) REVERT: B 582 ASP cc_start: 0.7830 (m-30) cc_final: 0.7322 (m-30) REVERT: B 701 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5974 (mp0) REVERT: B 705 THR cc_start: 0.6637 (OUTLIER) cc_final: 0.6195 (t) REVERT: C 218 ASP cc_start: 0.6156 (OUTLIER) cc_final: 0.5821 (m-30) REVERT: C 252 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.6917 (mt0) REVERT: C 314 HIS cc_start: 0.6859 (m-70) cc_final: 0.6079 (t-90) REVERT: C 370 SER cc_start: 0.5653 (m) cc_final: 0.5386 (p) REVERT: C 381 ILE cc_start: 0.7342 (tp) cc_final: 0.6894 (pt) REVERT: C 495 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7240 (tp40) REVERT: C 536 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7109 (mp-120) REVERT: C 544 GLU cc_start: 0.7660 (tt0) cc_final: 0.7340 (mt-10) REVERT: C 582 ASP cc_start: 0.7358 (m-30) cc_final: 0.6997 (m-30) REVERT: C 583 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7304 (m110) REVERT: C 655 LYS cc_start: 0.5512 (OUTLIER) cc_final: 0.5173 (mmtt) REVERT: C 710 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6407 (mt-10) REVERT: D 314 HIS cc_start: 0.6442 (m-70) cc_final: 0.5645 (t70) REVERT: D 318 ASP cc_start: 0.6349 (m-30) cc_final: 0.6116 (m-30) REVERT: D 376 ASN cc_start: 0.7289 (m-40) cc_final: 0.7012 (m-40) REVERT: D 452 MET cc_start: 0.8661 (ptt) cc_final: 0.8446 (ptt) REVERT: D 458 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.6498 (ttt-90) REVERT: D 568 ASP cc_start: 0.7153 (m-30) cc_final: 0.6867 (m-30) REVERT: D 660 MET cc_start: 0.5939 (tpt) cc_final: 0.5547 (tpt) REVERT: E 252 GLN cc_start: 0.7191 (mt0) cc_final: 0.6913 (mm110) REVERT: E 321 LYS cc_start: 0.6378 (ttpt) cc_final: 0.5602 (tttt) REVERT: E 589 LYS cc_start: 0.7632 (ttpp) cc_final: 0.7264 (tttm) REVERT: E 606 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: E 660 MET cc_start: 0.6298 (tpt) cc_final: 0.6007 (tpt) REVERT: F 218 ASP cc_start: 0.6571 (p0) cc_final: 0.6359 (p0) REVERT: F 314 HIS cc_start: 0.6332 (m-70) cc_final: 0.6046 (t70) REVERT: F 321 LYS cc_start: 0.6322 (tttm) cc_final: 0.6013 (ttpp) REVERT: F 325 ARG cc_start: 0.5158 (OUTLIER) cc_final: 0.4878 (tpp80) REVERT: F 373 GLU cc_start: 0.6143 (pt0) cc_final: 0.5878 (pt0) REVERT: F 426 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7483 (mm-30) REVERT: F 582 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6748 (t70) REVERT: F 583 ASN cc_start: 0.7753 (m110) cc_final: 0.7148 (t0) REVERT: F 706 LYS cc_start: 0.5861 (mtmt) cc_final: 0.5507 (mtmt) REVERT: F 707 PHE cc_start: 0.5667 (OUTLIER) cc_final: 0.3475 (p90) REVERT: F 722 GLU cc_start: 0.5850 (mm-30) cc_final: 0.5395 (mm-30) REVERT: G 426 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: G 583 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.6989 (t0) REVERT: G 667 LYS cc_start: 0.4893 (mtpp) cc_final: 0.4371 (mmpt) REVERT: H 51 LYS cc_start: 0.4777 (OUTLIER) cc_final: 0.4390 (mtpt) REVERT: H 60 TYR cc_start: 0.4079 (m-80) cc_final: 0.3116 (t80) REVERT: H 65 GLU cc_start: 0.4780 (mt-10) cc_final: 0.4088 (mm-30) REVERT: H 77 ARG cc_start: 0.5292 (ttp80) cc_final: 0.4995 (ttp80) REVERT: H 109 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6619 (tm-30) REVERT: H 143 GLU cc_start: 0.6415 (mt-10) cc_final: 0.6015 (mt-10) REVERT: H 156 MET cc_start: 0.7593 (mmm) cc_final: 0.6978 (mmm) REVERT: H 180 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6768 (tt0) REVERT: H 216 ASP cc_start: 0.5680 (m-30) cc_final: 0.4961 (p0) REVERT: H 247 MET cc_start: 0.4165 (tmm) cc_final: 0.2945 (tpp) REVERT: H 352 ARG cc_start: 0.2963 (mtt90) cc_final: 0.2741 (mtt-85) REVERT: H 372 ILE cc_start: 0.2548 (OUTLIER) cc_final: 0.2276 (pp) outliers start: 90 outliers final: 56 residues processed: 282 average time/residue: 1.1777 time to fit residues: 405.4383 Evaluate side-chains 284 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 209 time to evaluate : 3.871 ------------------------------------------------------------------------------- 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 544 GLU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain C residue 218 ASP 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 319 GLN Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 377 THR 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 542 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 654 THR 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 377 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 264 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 324 SER 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 661 SER 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 325 ARG 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 582 ASP Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 636 ASN 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 420 SER Chi-restraints excluded: chain G residue 426 GLU Chi-restraints excluded: chain G residue 583 ASN Chi-restraints excluded: chain H residue 50 SER 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 177 THR Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 324 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 0.0470 chunk 362 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 252 optimal weight: 0.0670 chunk 380 optimal weight: 0.9980 chunk 350 optimal weight: 0.0060 chunk 303 optimal weight: 0.0030 chunk 31 optimal weight: 0.9990 chunk 234 optimal weight: 0.2980 chunk 185 optimal weight: 6.9990 overall best weight: 0.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 463 ASN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN C 463 ASN C 602 ASN C 627 ASN E 265 ASN E 501 ASN F 463 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31177 Z= 0.126 Angle : 0.491 13.883 42251 Z= 0.261 Chirality : 0.044 0.165 4758 Planarity : 0.004 0.057 5493 Dihedral : 4.468 43.506 4207 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.47 % Allowed : 14.46 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3884 helix: 1.40 (0.22), residues: 589 sheet: 1.12 (0.16), residues: 1181 loop : -0.87 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 375 HIS 0.002 0.000 HIS H 157 PHE 0.021 0.001 PHE C 711 TYR 0.017 0.001 TYR B 704 ARG 0.004 0.000 ARG H 77 ********************** 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 299 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 3.617 Fit side-chains revert: symmetry clash REVERT: A 314 HIS cc_start: 0.6582 (m-70) cc_final: 0.5965 (t-90) REVERT: A 321 LYS cc_start: 0.5724 (ttpp) cc_final: 0.5123 (mtmt) REVERT: A 376 ASN cc_start: 0.7005 (m-40) cc_final: 0.6313 (t0) REVERT: B 263 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7317 (mm-30) REVERT: B 313 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7415 (mt-10) REVERT: B 318 ASP cc_start: 0.6115 (m-30) cc_final: 0.5649 (m-30) REVERT: B 376 ASN cc_start: 0.6699 (OUTLIER) cc_final: 0.6405 (t0) REVERT: B 582 ASP cc_start: 0.7734 (m-30) cc_final: 0.7207 (m-30) REVERT: B 705 THR cc_start: 0.6293 (OUTLIER) cc_final: 0.5946 (t) REVERT: C 218 ASP cc_start: 0.6098 (p0) cc_final: 0.5774 (m-30) REVERT: C 305 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7585 (mt-10) REVERT: C 314 HIS cc_start: 0.6834 (m-70) cc_final: 0.6080 (t-90) REVERT: C 318 ASP cc_start: 0.6192 (m-30) cc_final: 0.5768 (t70) REVERT: C 370 SER cc_start: 0.5737 (m) cc_final: 0.5527 (p) REVERT: C 381 ILE cc_start: 0.7361 (tp) cc_final: 0.6888 (pt) REVERT: C 468 LYS cc_start: 0.7689 (mmpt) cc_final: 0.7423 (mmpt) REVERT: C 536 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7159 (mp-120) REVERT: C 544 GLU cc_start: 0.7727 (tt0) cc_final: 0.7396 (mt-10) REVERT: C 582 ASP cc_start: 0.7335 (m-30) cc_final: 0.7045 (m-30) REVERT: D 217 GLU cc_start: 0.4752 (pp20) cc_final: 0.3977 (pp20) REVERT: D 304 MET cc_start: 0.8751 (ttp) cc_final: 0.8517 (ttp) REVERT: D 314 HIS cc_start: 0.6423 (m-70) cc_final: 0.5649 (t70) REVERT: D 318 ASP cc_start: 0.5980 (m-30) cc_final: 0.5766 (m-30) REVERT: D 382 ASN cc_start: 0.8068 (t0) cc_final: 0.7775 (t0) REVERT: D 452 MET cc_start: 0.8444 (ptt) cc_final: 0.8178 (ptt) REVERT: D 458 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.6596 (ttt-90) REVERT: D 568 ASP cc_start: 0.7103 (m-30) cc_final: 0.6817 (m-30) REVERT: D 660 MET cc_start: 0.5835 (tpt) cc_final: 0.5128 (tmt) REVERT: D 689 LYS cc_start: 0.5736 (tmtt) cc_final: 0.5307 (tmtt) REVERT: E 313 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6702 (mt-10) REVERT: E 319 GLN cc_start: 0.6600 (mt0) cc_final: 0.5862 (mt0) REVERT: E 321 LYS cc_start: 0.6317 (ttpt) cc_final: 0.6034 (ttmm) REVERT: E 376 ASN cc_start: 0.6864 (m-40) cc_final: 0.6401 (t0) REVERT: E 589 LYS cc_start: 0.7652 (ttpp) cc_final: 0.7239 (tttm) REVERT: E 606 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: E 660 MET cc_start: 0.6365 (tpt) cc_final: 0.5992 (tpt) REVERT: F 314 HIS cc_start: 0.6175 (m-70) cc_final: 0.5901 (t70) REVERT: F 319 GLN cc_start: 0.6572 (pt0) cc_final: 0.5981 (mt0) REVERT: F 373 GLU cc_start: 0.6192 (pt0) cc_final: 0.5901 (pt0) REVERT: F 426 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7452 (mm-30) REVERT: F 499 GLU cc_start: 0.7694 (tp30) cc_final: 0.7484 (tp30) REVERT: F 582 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6561 (t70) REVERT: F 583 ASN cc_start: 0.7701 (m110) cc_final: 0.7014 (t0) REVERT: F 707 PHE cc_start: 0.5493 (OUTLIER) cc_final: 0.3371 (p90) REVERT: G 376 ASN cc_start: 0.6808 (m-40) cc_final: 0.6540 (m-40) REVERT: G 583 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7253 (m110) REVERT: G 667 LYS cc_start: 0.4787 (mtpp) cc_final: 0.4439 (mmmt) REVERT: H 40 GLU cc_start: 0.5591 (mm-30) cc_final: 0.5364 (mm-30) REVERT: H 65 GLU cc_start: 0.4825 (mt-10) cc_final: 0.4196 (mm-30) REVERT: H 77 ARG cc_start: 0.5315 (ttp80) cc_final: 0.5081 (tmm-80) REVERT: H 109 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6613 (tm-30) REVERT: H 143 GLU cc_start: 0.6317 (mt-10) cc_final: 0.5919 (mt-10) REVERT: H 156 MET cc_start: 0.7485 (mmm) cc_final: 0.7030 (mmm) REVERT: H 216 ASP cc_start: 0.5553 (m-30) cc_final: 0.4832 (p0) REVERT: H 247 MET cc_start: 0.4379 (tmm) cc_final: 0.2860 (tpp) REVERT: H 372 ILE cc_start: 0.2398 (OUTLIER) cc_final: 0.2097 (mp) outliers start: 47 outliers final: 27 residues processed: 291 average time/residue: 1.1757 time to fit residues: 417.0653 Evaluate side-chains 263 residues out of total 3384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 228 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 319 GLN 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 376 ASN Chi-restraints excluded: chain B residue 705 THR 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 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 617 THR Chi-restraints excluded: chain D residue 672 SER Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 606 GLU Chi-restraints excluded: chain E residue 661 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 582 ASP 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 583 ASN Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 324 SER 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 240 optimal weight: 6.9990 chunk 322 optimal weight: 2.9990 chunk 92 optimal weight: 0.0370 chunk 279 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 84 optimal weight: 0.0040 chunk 303 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 311 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 overall best weight: 0.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 319 GLN B 463 ASN C 463 ASN C 627 ASN E 252 GLN E 634 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.158690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121878 restraints weight = 128054.298| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 5.81 r_work: 0.2903 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31177 Z= 0.127 Angle : 0.491 14.256 42251 Z= 0.263 Chirality : 0.043 0.157 4758 Planarity : 0.004 0.059 5493 Dihedral : 4.421 40.957 4207 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.13 % Allowed : 15.21 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3884 helix: 1.41 (0.22), residues: 595 sheet: 0.87 (0.16), residues: 1199 loop : -0.80 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 375 HIS 0.002 0.000 HIS H 157 PHE 0.022 0.001 PHE C 711 TYR 0.017 0.001 TYR B 704 ARG 0.005 0.000 ARG H 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9739.09 seconds wall clock time: 178 minutes 3.51 seconds (10683.51 seconds total)