Starting phenix.real_space_refine on Tue Mar 19 05:18:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/03_2024/3j9c_6224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/03_2024/3j9c_6224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/03_2024/3j9c_6224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/03_2024/3j9c_6224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/03_2024/3j9c_6224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/03_2024/3j9c_6224.pdb" } resolution = 2.9 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.016 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 14 9.91 5 S 35 5.16 5 C 14504 2.51 5 N 4046 2.21 5 O 4697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E GLU 515": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G GLU 515": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23296 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3328 Unusual residues: {' CA': 2} Classifications: {'peptide': 423, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403, None: 2} Not linked: pdbres="PHE A 596 " pdbres=" CA A 801 " Not linked: pdbres=" CA A 801 " pdbres=" CA A 802 " Chain: "B" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3328 Unusual residues: {' CA': 2} Classifications: {'peptide': 423, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403, None: 2} Not linked: pdbres="PHE B 596 " pdbres=" CA B 801 " Not linked: pdbres=" CA B 801 " pdbres=" CA B 802 " Chain: "C" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3328 Unusual residues: {' CA': 2} Classifications: {'peptide': 423, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403, None: 2} Not linked: pdbres="PHE C 596 " pdbres=" CA C 801 " Not linked: pdbres=" CA C 801 " pdbres=" CA C 802 " Chain: "D" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3328 Unusual residues: {' CA': 2} Classifications: {'peptide': 423, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403, None: 2} Not linked: pdbres="PHE D 596 " pdbres=" CA D 801 " Not linked: pdbres=" CA D 801 " pdbres=" CA D 802 " Chain: "E" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3328 Unusual residues: {' CA': 2} Classifications: {'peptide': 423, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403, None: 2} Not linked: pdbres="PHE E 596 " pdbres=" CA E 801 " Not linked: pdbres=" CA E 801 " pdbres=" CA E 802 " Chain: "F" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3328 Unusual residues: {' CA': 2} Classifications: {'peptide': 423, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403, None: 2} Not linked: pdbres="PHE F 596 " pdbres=" CA F 801 " Not linked: pdbres=" CA F 801 " pdbres=" CA F 802 " Chain: "G" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3328 Unusual residues: {' CA': 2} Classifications: {'peptide': 423, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 403, None: 2} Not linked: pdbres="PHE G 596 " pdbres=" CA G 801 " Not linked: pdbres=" CA G 801 " pdbres=" CA G 802 " Time building chain proxies: 12.04, per 1000 atoms: 0.52 Number of scatterers: 23296 At special positions: 0 Unit cell: (143.36, 140.8, 199.68, 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 14 19.99 S 35 16.00 O 4697 8.00 N 4046 7.00 C 14504 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: 8.61 Conformation dependent library (CDL) restraints added in 4.4 seconds 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5656 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 63 sheets defined 20.8% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS A 518 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR A 576 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 578 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 476 through 486 removed outlier: 3.821A pdb=" N VAL B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.610A pdb=" N LYS B 518 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR B 576 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 578 " --> pdb=" O TYR B 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 476 through 486 removed outlier: 3.821A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS C 518 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 532 Processing helix chain 'C' and resid 555 through 569 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR C 576 " --> pdb=" O ASN C 573 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 578 " --> pdb=" O TYR C 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) Proline residue: D 482 - end of helix Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 532 Processing helix chain 'D' and resid 555 through 569 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR D 576 " --> pdb=" O ASN D 573 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU D 578 " --> pdb=" O TYR D 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Proline residue: E 482 - end of helix Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS E 518 " --> pdb=" O GLU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 Processing helix chain 'E' and resid 555 through 569 Processing helix chain 'E' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR E 576 " --> pdb=" O ASN E 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU E 578 " --> pdb=" O TYR E 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Proline residue: F 482 - end of helix Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS F 518 " --> pdb=" O GLU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 532 Processing helix chain 'F' and resid 555 through 569 Processing helix chain 'F' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR F 576 " --> pdb=" O ASN F 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU F 578 " --> pdb=" O TYR F 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL G 480 " --> pdb=" O ASN G 476 " (cutoff:3.500A) Proline residue: G 482 - end of helix Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS G 518 " --> pdb=" O GLU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 Processing helix chain 'G' and resid 555 through 569 Processing helix chain 'G' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR G 576 " --> pdb=" O ASN G 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU G 578 " --> pdb=" O TYR G 575 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 192 through 196 Processing sheet with id= 2, first strand: chain 'A' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL A 264 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 367 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET A 266 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG A 365 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 268 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 432 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 276 through 299 Processing sheet with id= 5, first strand: chain 'A' and resid 302 through 311 Processing sheet with id= 6, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN A 376 " --> pdb=" O ASN A 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN A 458 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 454 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER A 382 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR A 452 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 384 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A 450 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 460 through 462 Processing sheet with id= 8, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 541 through 542 Processing sheet with id= 10, first strand: chain 'B' and resid 192 through 196 Processing sheet with id= 11, first strand: chain 'B' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL B 264 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 367 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET B 266 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG B 365 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 268 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 276 through 299 Processing sheet with id= 14, first strand: chain 'B' and resid 302 through 311 Processing sheet with id= 15, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN B 376 " --> pdb=" O ASN B 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN B 458 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 454 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER B 382 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR B 452 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 384 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 450 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 460 through 462 Processing sheet with id= 17, first strand: chain 'B' and resid 501 through 506 removed outlier: 8.445A pdb=" N ILE B 589 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 541 through 542 Processing sheet with id= 19, first strand: chain 'C' and resid 192 through 196 Processing sheet with id= 20, first strand: chain 'C' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL C 264 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 367 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N MET C 266 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG C 365 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 268 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 409 through 411 removed outlier: 3.799A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 432 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 276 through 299 Processing sheet with id= 23, first strand: chain 'C' and resid 302 through 311 Processing sheet with id= 24, first strand: chain 'C' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN C 376 " --> pdb=" O ASN C 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN C 458 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN C 454 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER C 382 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR C 452 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C 384 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU C 450 " --> pdb=" O VAL C 384 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 460 through 462 Processing sheet with id= 26, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 541 through 542 Processing sheet with id= 28, first strand: chain 'D' and resid 192 through 196 Processing sheet with id= 29, first strand: chain 'D' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL D 264 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL D 367 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET D 266 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG D 365 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D 268 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.799A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE D 432 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 276 through 299 Processing sheet with id= 32, first strand: chain 'D' and resid 302 through 311 Processing sheet with id= 33, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN D 376 " --> pdb=" O ASN D 458 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASN D 458 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 454 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER D 382 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR D 452 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL D 384 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D 450 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 460 through 462 Processing sheet with id= 35, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 541 through 542 Processing sheet with id= 37, first strand: chain 'E' and resid 192 through 196 Processing sheet with id= 38, first strand: chain 'E' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL E 264 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL E 367 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET E 266 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG E 365 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 268 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'E' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE E 432 " --> pdb=" O LEU E 360 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'E' and resid 276 through 299 Processing sheet with id= 41, first strand: chain 'E' and resid 302 through 311 Processing sheet with id= 42, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN E 376 " --> pdb=" O ASN E 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN E 458 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN E 454 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER E 382 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR E 452 " --> pdb=" O SER E 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL E 384 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU E 450 " --> pdb=" O VAL E 384 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'E' and resid 460 through 462 Processing sheet with id= 44, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 541 through 542 Processing sheet with id= 46, first strand: chain 'F' and resid 192 through 196 Processing sheet with id= 47, first strand: chain 'F' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL F 264 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL F 367 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET F 266 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG F 365 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 268 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'F' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE F 432 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'F' and resid 276 through 299 Processing sheet with id= 50, first strand: chain 'F' and resid 302 through 311 Processing sheet with id= 51, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN F 376 " --> pdb=" O ASN F 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN F 458 " --> pdb=" O ASN F 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN F 454 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER F 382 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR F 452 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL F 384 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU F 450 " --> pdb=" O VAL F 384 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'F' and resid 460 through 462 Processing sheet with id= 53, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'F' and resid 541 through 542 Processing sheet with id= 55, first strand: chain 'G' and resid 192 through 196 Processing sheet with id= 56, first strand: chain 'G' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL G 264 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL G 367 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N MET G 266 " --> pdb=" O ARG G 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG G 365 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN G 268 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'G' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE G 432 " --> pdb=" O LEU G 360 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'G' and resid 276 through 299 Processing sheet with id= 59, first strand: chain 'G' and resid 302 through 311 Processing sheet with id= 60, first strand: chain 'G' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN G 376 " --> pdb=" O ASN G 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN G 458 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN G 454 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER G 382 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR G 452 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL G 384 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU G 450 " --> pdb=" O VAL G 384 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'G' and resid 460 through 462 Processing sheet with id= 62, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.445A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'G' and resid 541 through 542 805 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 9.32 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: 7766 1.34 - 1.45: 2865 1.45 - 1.57: 13001 1.57 - 1.69: 7 1.69 - 1.81: 70 Bond restraints: 23709 Sorted by residual: bond pdb=" CA LYS F 444 " pdb=" C LYS F 444 " ideal model delta sigma weight residual 1.523 1.606 -0.082 1.34e-02 5.57e+03 3.78e+01 bond pdb=" CA LYS D 444 " pdb=" C LYS D 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.75e+01 bond pdb=" CA LYS E 444 " pdb=" C LYS E 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.73e+01 bond pdb=" CA LYS G 444 " pdb=" C LYS G 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.73e+01 bond pdb=" CA LYS A 444 " pdb=" C LYS A 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.72e+01 ... (remaining 23704 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.16: 618 106.16 - 113.12: 12895 113.12 - 120.07: 7509 120.07 - 127.03: 11064 127.03 - 133.98: 142 Bond angle restraints: 32228 Sorted by residual: angle pdb=" C ALA G 417 " pdb=" N PRO G 418 " pdb=" CA PRO G 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.97e+01 angle pdb=" C ALA B 417 " pdb=" N PRO B 418 " pdb=" CA PRO B 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.97e+01 angle pdb=" C ALA C 417 " pdb=" N PRO C 418 " pdb=" CA PRO C 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.96e+01 angle pdb=" C ALA A 417 " pdb=" N PRO A 418 " pdb=" CA PRO A 418 " ideal model delta sigma weight residual 119.78 125.37 -5.59 1.03e+00 9.43e-01 2.95e+01 angle pdb=" C ALA E 417 " pdb=" N PRO E 418 " pdb=" CA PRO E 418 " ideal model delta sigma weight residual 119.78 125.37 -5.59 1.03e+00 9.43e-01 2.94e+01 ... (remaining 32223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.73: 12750 13.73 - 27.45: 1068 27.45 - 41.17: 378 41.17 - 54.90: 189 54.90 - 68.62: 84 Dihedral angle restraints: 14469 sinusoidal: 5768 harmonic: 8701 Sorted by residual: dihedral pdb=" CA SER D 413 " pdb=" C SER D 413 " pdb=" N LYS D 414 " pdb=" CA LYS D 414 " ideal model delta harmonic sigma weight residual 180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER G 413 " pdb=" C SER G 413 " pdb=" N LYS G 414 " pdb=" CA LYS G 414 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER B 413 " pdb=" C SER B 413 " pdb=" N LYS B 414 " pdb=" CA LYS B 414 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 14466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2892 0.050 - 0.100: 611 0.100 - 0.150: 172 0.150 - 0.200: 7 0.200 - 0.249: 14 Chirality restraints: 3696 Sorted by residual: chirality pdb=" CA LYS E 444 " pdb=" N LYS E 444 " pdb=" C LYS E 444 " pdb=" CB LYS E 444 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA LYS D 444 " pdb=" N LYS D 444 " pdb=" C LYS D 444 " pdb=" CB LYS D 444 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA GLN D 543 " pdb=" N GLN D 543 " pdb=" C GLN D 543 " pdb=" CB GLN D 543 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3693 not shown) Planarity restraints: 4249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 378 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO E 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 379 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 378 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO B 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 379 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 378 " 0.028 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO F 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO F 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 379 " 0.024 5.00e-02 4.00e+02 ... (remaining 4246 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6068 2.80 - 3.33: 21651 3.33 - 3.85: 40621 3.85 - 4.38: 48843 4.38 - 4.90: 82492 Nonbonded interactions: 199675 Sorted by model distance: nonbonded pdb=" O ILE C 183 " pdb="CA CA C 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE F 183 " pdb="CA CA F 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE E 183 " pdb="CA CA E 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE D 183 " pdb="CA CA D 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE A 183 " pdb="CA CA A 801 " model vdw 2.277 2.510 ... (remaining 199670 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 0.020 Extract box with map and model: 2.490 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 59.170 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:14.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.005 0.082 23709 Z= 0.353 Angle : 1.112 10.831 32228 Z= 0.743 Chirality : 0.047 0.249 3696 Planarity : 0.004 0.043 4249 Dihedral : 14.410 68.624 8813 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.13 % Allowed : 8.27 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.81 (0.16), residues: 2947 helix: -1.67 (0.20), residues: 497 sheet: -0.98 (0.15), residues: 1001 loop : 0.51 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 226 HIS 0.003 0.001 HIS D 263 PHE 0.011 0.001 PHE D 493 TYR 0.013 0.002 TYR B 456 ARG 0.003 0.001 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 600 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.6849 (mt0) cc_final: 0.6557 (mm110) REVERT: A 287 ARG cc_start: 0.6325 (mtt90) cc_final: 0.5455 (ttp-170) REVERT: A 291 LYS cc_start: 0.6378 (tptt) cc_final: 0.5327 (tmtt) REVERT: A 330 SER cc_start: 0.4698 (OUTLIER) cc_final: 0.4233 (p) REVERT: A 334 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6509 (mt) REVERT: A 343 GLU cc_start: 0.7844 (tt0) cc_final: 0.7613 (tt0) REVERT: A 344 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.6822 (ttp80) REVERT: A 348 GLU cc_start: 0.7973 (tt0) cc_final: 0.7746 (pt0) REVERT: A 350 MET cc_start: 0.8690 (mmm) cc_final: 0.7772 (ttp) REVERT: A 387 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8033 (ttpp) REVERT: A 388 ASN cc_start: 0.8794 (p0) cc_final: 0.8302 (p0) REVERT: A 404 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8834 (tp) REVERT: A 434 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8578 (ttp) REVERT: A 436 TYR cc_start: 0.8663 (t80) cc_final: 0.8337 (t80) REVERT: A 441 GLU cc_start: 0.8347 (tt0) cc_final: 0.7965 (mt-10) REVERT: A 447 GLN cc_start: 0.7028 (mt0) cc_final: 0.6791 (mp10) REVERT: A 465 GLU cc_start: 0.9131 (tt0) cc_final: 0.8657 (mm-30) REVERT: A 470 ARG cc_start: 0.8906 (mtt180) cc_final: 0.8409 (ptp90) REVERT: A 486 GLU cc_start: 0.9036 (tp30) cc_final: 0.8790 (mm-30) REVERT: A 542 TYR cc_start: 0.8931 (t80) cc_final: 0.8319 (t80) REVERT: A 579 ASP cc_start: 0.8595 (p0) cc_final: 0.8303 (t0) REVERT: A 580 LYS cc_start: 0.8917 (mttp) cc_final: 0.8653 (mptt) REVERT: A 586 LYS cc_start: 0.8869 (mttm) cc_final: 0.8294 (mtpt) REVERT: A 595 ARG cc_start: 0.7691 (mtm180) cc_final: 0.7417 (mtm180) REVERT: B 212 GLU cc_start: 0.8218 (tt0) cc_final: 0.7968 (tm-30) REVERT: B 263 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8750 (p90) REVERT: B 285 GLN cc_start: 0.6923 (mt0) cc_final: 0.6677 (mm-40) REVERT: B 287 ARG cc_start: 0.6382 (mtt90) cc_final: 0.5504 (ttp-170) REVERT: B 291 LYS cc_start: 0.6358 (tptt) cc_final: 0.6106 (tmtm) REVERT: B 330 SER cc_start: 0.5150 (OUTLIER) cc_final: 0.4812 (p) REVERT: B 334 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6496 (mt) REVERT: B 344 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.6430 (tmt170) REVERT: B 348 GLU cc_start: 0.8094 (tt0) cc_final: 0.7795 (pt0) REVERT: B 350 MET cc_start: 0.8513 (mmm) cc_final: 0.7413 (pp-130) REVERT: B 387 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8280 (tmmt) REVERT: B 403 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9079 (mt0) REVERT: B 404 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.8867 (tp) REVERT: B 414 LYS cc_start: 0.9061 (tptt) cc_final: 0.8793 (tppp) REVERT: B 434 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8727 (ttp) REVERT: B 436 TYR cc_start: 0.8613 (t80) cc_final: 0.8364 (t80) REVERT: B 441 GLU cc_start: 0.8208 (tt0) cc_final: 0.7619 (tp30) REVERT: B 446 LYS cc_start: 0.7672 (mmtp) cc_final: 0.7124 (tptp) REVERT: B 447 GLN cc_start: 0.7238 (mt0) cc_final: 0.6675 (mp10) REVERT: B 462 TYR cc_start: 0.8981 (t80) cc_final: 0.8675 (t80) REVERT: B 465 GLU cc_start: 0.9093 (tt0) cc_final: 0.8583 (mm-30) REVERT: B 470 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8432 (mmm160) REVERT: B 500 LEU cc_start: 0.8730 (mt) cc_final: 0.8526 (mm) REVERT: B 545 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8032 (ttpp) REVERT: B 560 GLN cc_start: 0.8312 (tp-100) cc_final: 0.8026 (tp40) REVERT: B 579 ASP cc_start: 0.8446 (p0) cc_final: 0.8124 (t0) REVERT: B 595 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7845 (mtm180) REVERT: C 285 GLN cc_start: 0.6860 (mt0) cc_final: 0.6548 (mm-40) REVERT: C 287 ARG cc_start: 0.6458 (mtt90) cc_final: 0.5597 (ttp-110) REVERT: C 291 LYS cc_start: 0.5830 (tptt) cc_final: 0.5430 (tttm) REVERT: C 330 SER cc_start: 0.4677 (OUTLIER) cc_final: 0.4134 (p) REVERT: C 344 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.6957 (ttp80) REVERT: C 350 MET cc_start: 0.8618 (mmm) cc_final: 0.7502 (tmt) REVERT: C 381 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8727 (p) REVERT: C 387 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8220 (ttpp) REVERT: C 404 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8658 (tp) REVERT: C 434 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8743 (ttp) REVERT: C 436 TYR cc_start: 0.8803 (t80) cc_final: 0.8467 (t80) REVERT: C 441 GLU cc_start: 0.8416 (tt0) cc_final: 0.7897 (tm-30) REVERT: C 447 GLN cc_start: 0.7330 (mt0) cc_final: 0.6789 (mp10) REVERT: C 465 GLU cc_start: 0.9147 (tt0) cc_final: 0.8642 (mm-30) REVERT: C 470 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8494 (ptm160) REVERT: C 521 MET cc_start: 0.8982 (tpp) cc_final: 0.8744 (tpp) REVERT: C 539 ASN cc_start: 0.7195 (m110) cc_final: 0.6955 (p0) REVERT: C 579 ASP cc_start: 0.8471 (p0) cc_final: 0.8186 (t0) REVERT: C 586 LYS cc_start: 0.8744 (mttm) cc_final: 0.8352 (mtpt) REVERT: C 587 MET cc_start: 0.8769 (mtt) cc_final: 0.8491 (mtp) REVERT: D 285 GLN cc_start: 0.7118 (mt0) cc_final: 0.6693 (mm-40) REVERT: D 287 ARG cc_start: 0.6525 (mtt90) cc_final: 0.5667 (ttp-110) REVERT: D 330 SER cc_start: 0.5099 (OUTLIER) cc_final: 0.4301 (p) REVERT: D 334 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6457 (mt) REVERT: D 340 LEU cc_start: 0.7542 (mt) cc_final: 0.7138 (mm) REVERT: D 344 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.6991 (ttp-170) REVERT: D 387 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8266 (ttpt) REVERT: D 388 ASN cc_start: 0.8706 (p0) cc_final: 0.8490 (p0) REVERT: D 398 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8925 (pm20) REVERT: D 403 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.9108 (mt0) REVERT: D 404 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8829 (tp) REVERT: D 434 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8608 (ttp) REVERT: D 441 GLU cc_start: 0.8137 (tt0) cc_final: 0.7630 (tm-30) REVERT: D 447 GLN cc_start: 0.6923 (mt0) cc_final: 0.6472 (mp10) REVERT: D 448 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8452 (tp) REVERT: D 465 GLU cc_start: 0.9117 (tt0) cc_final: 0.8670 (mm-30) REVERT: D 557 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8328 (tp-100) REVERT: D 579 ASP cc_start: 0.8428 (p0) cc_final: 0.8206 (t0) REVERT: D 587 MET cc_start: 0.8856 (mtt) cc_final: 0.8416 (mtm) REVERT: E 209 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.6895 (p0) REVERT: E 285 GLN cc_start: 0.7089 (mt0) cc_final: 0.6840 (mm110) REVERT: E 287 ARG cc_start: 0.6467 (mtt90) cc_final: 0.5447 (ttp-110) REVERT: E 291 LYS cc_start: 0.6195 (tptt) cc_final: 0.5264 (tttt) REVERT: E 294 SER cc_start: 0.6521 (OUTLIER) cc_final: 0.6025 (t) REVERT: E 330 SER cc_start: 0.5383 (OUTLIER) cc_final: 0.4531 (p) REVERT: E 344 ARG cc_start: 0.7207 (ttp-110) cc_final: 0.6388 (ttp80) REVERT: E 348 GLU cc_start: 0.8101 (tt0) cc_final: 0.7892 (pt0) REVERT: E 350 MET cc_start: 0.8752 (mmm) cc_final: 0.7947 (ttp) REVERT: E 404 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8768 (tp) REVERT: E 434 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8678 (ttp) REVERT: E 441 GLU cc_start: 0.8344 (tt0) cc_final: 0.8007 (mt-10) REVERT: E 447 GLN cc_start: 0.7191 (mt0) cc_final: 0.6753 (mp10) REVERT: E 465 GLU cc_start: 0.9114 (tt0) cc_final: 0.8728 (mm-30) REVERT: E 470 ARG cc_start: 0.8783 (mtt180) cc_final: 0.8376 (mmm160) REVERT: E 542 TYR cc_start: 0.8790 (t80) cc_final: 0.8490 (t80) REVERT: E 545 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7437 (ttpt) REVERT: E 551 ASP cc_start: 0.8890 (p0) cc_final: 0.8519 (t0) REVERT: E 557 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7968 (tp-100) REVERT: E 560 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7409 (tm-30) REVERT: E 579 ASP cc_start: 0.8570 (p0) cc_final: 0.8214 (t0) REVERT: E 580 LYS cc_start: 0.8932 (mttp) cc_final: 0.8575 (mptt) REVERT: F 209 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7566 (p0) REVERT: F 212 GLU cc_start: 0.8409 (tt0) cc_final: 0.8184 (tm-30) REVERT: F 263 HIS cc_start: 0.9067 (OUTLIER) cc_final: 0.8823 (p90) REVERT: F 285 GLN cc_start: 0.6997 (mt0) cc_final: 0.6574 (mm-40) REVERT: F 287 ARG cc_start: 0.6452 (mtt90) cc_final: 0.5227 (tmt170) REVERT: F 294 SER cc_start: 0.6083 (OUTLIER) cc_final: 0.5649 (t) REVERT: F 330 SER cc_start: 0.4669 (OUTLIER) cc_final: 0.4152 (p) REVERT: F 344 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.6669 (ttp80) REVERT: F 350 MET cc_start: 0.8731 (mmm) cc_final: 0.7853 (ttp) REVERT: F 404 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8793 (tp) REVERT: F 434 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8637 (ttp) REVERT: F 441 GLU cc_start: 0.8511 (tt0) cc_final: 0.7994 (tm-30) REVERT: F 444 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7643 (mtpp) REVERT: F 447 GLN cc_start: 0.7104 (mt0) cc_final: 0.6758 (mp10) REVERT: F 465 GLU cc_start: 0.9112 (tt0) cc_final: 0.8646 (mm-30) REVERT: F 486 GLU cc_start: 0.9079 (tp30) cc_final: 0.8857 (mm-30) REVERT: F 579 ASP cc_start: 0.8521 (p0) cc_final: 0.8216 (t0) REVERT: F 586 LYS cc_start: 0.8708 (mttm) cc_final: 0.8230 (mtpt) REVERT: G 285 GLN cc_start: 0.6917 (mt0) cc_final: 0.6673 (mm110) REVERT: G 287 ARG cc_start: 0.6371 (mtt90) cc_final: 0.5357 (ttp-170) REVERT: G 291 LYS cc_start: 0.6560 (tptt) cc_final: 0.6271 (tmtp) REVERT: G 294 SER cc_start: 0.5544 (OUTLIER) cc_final: 0.4889 (t) REVERT: G 334 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6720 (mt) REVERT: G 344 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.6743 (ttp80) REVERT: G 350 MET cc_start: 0.8716 (mmm) cc_final: 0.7857 (ttp) REVERT: G 387 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (ttpp) REVERT: G 404 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8847 (tp) REVERT: G 434 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8629 (ttp) REVERT: G 441 GLU cc_start: 0.8407 (tt0) cc_final: 0.8039 (mt-10) REVERT: G 447 GLN cc_start: 0.6833 (mt0) cc_final: 0.6484 (mp10) REVERT: G 448 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8635 (tp) REVERT: G 465 GLU cc_start: 0.9108 (tt0) cc_final: 0.8718 (mm-30) REVERT: G 500 LEU cc_start: 0.8851 (mt) cc_final: 0.8591 (mm) REVERT: G 579 ASP cc_start: 0.8757 (p0) cc_final: 0.8297 (t0) REVERT: G 580 LYS cc_start: 0.8985 (mttp) cc_final: 0.8773 (mmtm) REVERT: G 587 MET cc_start: 0.8769 (mtt) cc_final: 0.8526 (mtm) outliers start: 161 outliers final: 17 residues processed: 706 average time/residue: 1.3811 time to fit residues: 1107.5494 Evaluate side-chains 415 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 355 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 263 HIS Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 557 GLN Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 294 SER Chi-restraints excluded: chain F residue 330 SER Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 387 LYS Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 123 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 140 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 266 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 483 GLN A 499 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN B 274 ASN B 483 GLN B 557 GLN C 389 GLN C 483 GLN D 274 ASN D 424 GLN D 499 ASN ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS E 274 ASN E 389 GLN E 424 GLN E 483 GLN E 570 ASN F 274 ASN F 389 GLN F 483 GLN F 499 ASN G 209 ASN G 274 ASN G 424 GLN G 483 GLN G 560 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23709 Z= 0.349 Angle : 0.597 5.794 32228 Z= 0.322 Chirality : 0.048 0.164 3696 Planarity : 0.005 0.040 4249 Dihedral : 7.996 58.855 3281 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.84 % Allowed : 14.78 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.32 (0.15), residues: 2947 helix: -0.36 (0.24), residues: 497 sheet: 0.16 (0.17), residues: 847 loop : -0.27 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 226 HIS 0.012 0.001 HIS E 263 PHE 0.014 0.002 PHE B 493 TYR 0.011 0.002 TYR F 233 ARG 0.004 0.000 ARG G 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 341 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.6947 (mt0) cc_final: 0.6642 (mm110) REVERT: A 287 ARG cc_start: 0.5924 (mtt90) cc_final: 0.5230 (ttp-170) REVERT: A 344 ARG cc_start: 0.7627 (ttp-110) cc_final: 0.6767 (ttp80) REVERT: A 348 GLU cc_start: 0.7991 (tt0) cc_final: 0.7260 (tm-30) REVERT: A 350 MET cc_start: 0.8458 (mmm) cc_final: 0.7605 (tmt) REVERT: A 387 LYS cc_start: 0.8381 (tptm) cc_final: 0.8130 (ttpp) REVERT: A 404 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.8853 (tp) REVERT: A 434 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8591 (ttp) REVERT: A 441 GLU cc_start: 0.8451 (tt0) cc_final: 0.7978 (tm-30) REVERT: A 447 GLN cc_start: 0.7323 (mt0) cc_final: 0.6958 (mp10) REVERT: A 465 GLU cc_start: 0.9030 (tt0) cc_final: 0.8631 (mm-30) REVERT: A 470 ARG cc_start: 0.8931 (mtt180) cc_final: 0.8412 (ptt90) REVERT: A 497 ASP cc_start: 0.8214 (m-30) cc_final: 0.7841 (p0) REVERT: A 545 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8015 (mtpt) REVERT: A 560 GLN cc_start: 0.8657 (tp40) cc_final: 0.8365 (tp40) REVERT: A 575 TYR cc_start: 0.8399 (m-80) cc_final: 0.8188 (m-80) REVERT: A 579 ASP cc_start: 0.8720 (p0) cc_final: 0.8179 (t0) REVERT: A 586 LYS cc_start: 0.9021 (mttm) cc_final: 0.8610 (mtpp) REVERT: A 595 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7401 (mtm180) REVERT: B 285 GLN cc_start: 0.7078 (mt0) cc_final: 0.6844 (mm-40) REVERT: B 287 ARG cc_start: 0.6072 (mtt90) cc_final: 0.5181 (ttp-170) REVERT: B 334 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6187 (pp) REVERT: B 344 ARG cc_start: 0.7377 (ttp-110) cc_final: 0.6340 (tmt170) REVERT: B 348 GLU cc_start: 0.8076 (tt0) cc_final: 0.7725 (pt0) REVERT: B 350 MET cc_start: 0.8310 (mmm) cc_final: 0.7605 (tmt) REVERT: B 387 LYS cc_start: 0.8580 (tptm) cc_final: 0.8316 (tmmt) REVERT: B 403 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.9116 (mt0) REVERT: B 404 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8812 (tp) REVERT: B 441 GLU cc_start: 0.8328 (tt0) cc_final: 0.8044 (tt0) REVERT: B 447 GLN cc_start: 0.7418 (mt0) cc_final: 0.6890 (mp10) REVERT: B 465 GLU cc_start: 0.9083 (tt0) cc_final: 0.8588 (mm-30) REVERT: B 470 ARG cc_start: 0.8846 (mtt180) cc_final: 0.8545 (mtp-110) REVERT: B 557 GLN cc_start: 0.8530 (tp40) cc_final: 0.8087 (tp-100) REVERT: B 560 GLN cc_start: 0.8596 (tp-100) cc_final: 0.8349 (tp40) REVERT: B 579 ASP cc_start: 0.8669 (p0) cc_final: 0.8259 (t0) REVERT: C 285 GLN cc_start: 0.6804 (mt0) cc_final: 0.6484 (mm-40) REVERT: C 287 ARG cc_start: 0.5869 (mtt90) cc_final: 0.4963 (ttp-110) REVERT: C 344 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.6864 (ttp80) REVERT: C 350 MET cc_start: 0.8415 (mmm) cc_final: 0.7508 (tmt) REVERT: C 394 ILE cc_start: 0.9395 (mp) cc_final: 0.9149 (mm) REVERT: C 404 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8592 (tp) REVERT: C 441 GLU cc_start: 0.8564 (tt0) cc_final: 0.7940 (tm-30) REVERT: C 447 GLN cc_start: 0.7663 (mt0) cc_final: 0.7063 (mp10) REVERT: C 465 GLU cc_start: 0.9096 (tt0) cc_final: 0.8619 (mm-30) REVERT: C 470 ARG cc_start: 0.8825 (mtt180) cc_final: 0.8523 (ptm160) REVERT: C 539 ASN cc_start: 0.7452 (m110) cc_final: 0.7095 (p0) REVERT: C 545 LYS cc_start: 0.8350 (mtpp) cc_final: 0.8001 (mtpt) REVERT: C 579 ASP cc_start: 0.8797 (p0) cc_final: 0.8443 (t0) REVERT: C 586 LYS cc_start: 0.8984 (mttm) cc_final: 0.8498 (mtpt) REVERT: C 587 MET cc_start: 0.8884 (mtt) cc_final: 0.8509 (mtp) REVERT: C 595 ARG cc_start: 0.7937 (mtm180) cc_final: 0.7396 (ptt180) REVERT: D 180 ASN cc_start: 0.9343 (t0) cc_final: 0.8981 (t0) REVERT: D 285 GLN cc_start: 0.6897 (mt0) cc_final: 0.6501 (mm110) REVERT: D 287 ARG cc_start: 0.5878 (mtt90) cc_final: 0.5098 (ttp-110) REVERT: D 297 ARG cc_start: 0.4967 (OUTLIER) cc_final: 0.4552 (mmt90) REVERT: D 334 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.6177 (pp) REVERT: D 340 LEU cc_start: 0.7282 (mt) cc_final: 0.7059 (mm) REVERT: D 344 ARG cc_start: 0.7553 (ttp-110) cc_final: 0.6791 (ttp-170) REVERT: D 387 LYS cc_start: 0.8571 (tptm) cc_final: 0.8348 (ttpt) REVERT: D 398 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8853 (mp0) REVERT: D 403 GLN cc_start: 0.9433 (OUTLIER) cc_final: 0.8994 (mt0) REVERT: D 404 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8819 (tp) REVERT: D 434 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8493 (ttp) REVERT: D 441 GLU cc_start: 0.8216 (tt0) cc_final: 0.7752 (tm-30) REVERT: D 447 GLN cc_start: 0.7329 (mt0) cc_final: 0.6836 (mp10) REVERT: D 465 GLU cc_start: 0.9107 (tt0) cc_final: 0.8893 (tm-30) REVERT: D 557 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8008 (tp-100) REVERT: D 579 ASP cc_start: 0.8580 (p0) cc_final: 0.8232 (t0) REVERT: D 587 MET cc_start: 0.8829 (mtt) cc_final: 0.8617 (mtp) REVERT: E 209 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.6821 (p0) REVERT: E 285 GLN cc_start: 0.6693 (mt0) cc_final: 0.6473 (mm-40) REVERT: E 287 ARG cc_start: 0.6106 (mtt90) cc_final: 0.5330 (ttp-110) REVERT: E 344 ARG cc_start: 0.7201 (ttp-110) cc_final: 0.6305 (ttp80) REVERT: E 348 GLU cc_start: 0.7982 (tt0) cc_final: 0.7701 (pt0) REVERT: E 350 MET cc_start: 0.8600 (mmm) cc_final: 0.7964 (ttp) REVERT: E 403 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.8793 (mt0) REVERT: E 404 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8641 (tp) REVERT: E 441 GLU cc_start: 0.8507 (tt0) cc_final: 0.7817 (tm-30) REVERT: E 447 GLN cc_start: 0.7236 (mt0) cc_final: 0.6788 (mp10) REVERT: E 465 GLU cc_start: 0.9122 (tt0) cc_final: 0.8664 (mm-30) REVERT: E 542 TYR cc_start: 0.8818 (t80) cc_final: 0.8560 (t80) REVERT: E 557 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8135 (tp-100) REVERT: E 560 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8166 (tp40) REVERT: E 579 ASP cc_start: 0.8665 (p0) cc_final: 0.8228 (t0) REVERT: F 209 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7423 (p0) REVERT: F 285 GLN cc_start: 0.6745 (mt0) cc_final: 0.6421 (mm110) REVERT: F 330 SER cc_start: 0.4407 (m) cc_final: 0.3991 (t) REVERT: F 344 ARG cc_start: 0.7374 (ttp-110) cc_final: 0.6640 (ttp80) REVERT: F 404 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8767 (tp) REVERT: F 434 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8538 (ttp) REVERT: F 441 GLU cc_start: 0.8487 (tt0) cc_final: 0.7881 (tm-30) REVERT: F 444 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7760 (mtpp) REVERT: F 447 GLN cc_start: 0.7209 (mt0) cc_final: 0.6858 (mp10) REVERT: F 465 GLU cc_start: 0.9180 (tt0) cc_final: 0.8651 (mm-30) REVERT: F 486 GLU cc_start: 0.9185 (tp30) cc_final: 0.8942 (mm-30) REVERT: F 497 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8111 (p0) REVERT: F 560 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8181 (tp-100) REVERT: F 579 ASP cc_start: 0.8858 (p0) cc_final: 0.8464 (t0) REVERT: F 586 LYS cc_start: 0.8929 (mttm) cc_final: 0.8523 (mtpt) REVERT: F 595 ARG cc_start: 0.7387 (mtm180) cc_final: 0.6862 (ptt-90) REVERT: G 285 GLN cc_start: 0.6880 (mt0) cc_final: 0.6642 (mm110) REVERT: G 287 ARG cc_start: 0.5957 (mtt90) cc_final: 0.5022 (ttp-170) REVERT: G 334 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6418 (pp) REVERT: G 340 LEU cc_start: 0.7539 (mt) cc_final: 0.7239 (mm) REVERT: G 344 ARG cc_start: 0.7586 (ttp-110) cc_final: 0.6645 (tmt170) REVERT: G 350 MET cc_start: 0.8548 (mmm) cc_final: 0.7754 (ttp) REVERT: G 403 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.9021 (mt0) REVERT: G 404 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8761 (tp) REVERT: G 441 GLU cc_start: 0.8531 (tt0) cc_final: 0.8154 (mt-10) REVERT: G 447 GLN cc_start: 0.7122 (mt0) cc_final: 0.6897 (mp10) REVERT: G 448 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8518 (tt) REVERT: G 465 GLU cc_start: 0.9136 (tt0) cc_final: 0.8757 (mm-30) REVERT: G 497 ASP cc_start: 0.8382 (m-30) cc_final: 0.8015 (p0) REVERT: G 500 LEU cc_start: 0.9042 (mt) cc_final: 0.8768 (mm) REVERT: G 557 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8232 (tp-100) REVERT: G 579 ASP cc_start: 0.8672 (p0) cc_final: 0.8305 (t70) REVERT: G 587 MET cc_start: 0.8883 (mtt) cc_final: 0.8615 (mtm) REVERT: G 595 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7138 (ptt-90) outliers start: 127 outliers final: 54 residues processed: 412 average time/residue: 1.5147 time to fit residues: 702.1147 Evaluate side-chains 379 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 303 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 414 LYS Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 562 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 181 optimal weight: 50.0000 chunk 73 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 265 optimal weight: 40.0000 chunk 91 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 476 ASN C 476 ASN D 424 GLN D 476 ASN ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 GLN E 476 ASN F 389 GLN F 476 ASN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN G 537 ASN G 541 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 23709 Z= 0.431 Angle : 0.602 6.063 32228 Z= 0.320 Chirality : 0.050 0.165 3696 Planarity : 0.005 0.048 4249 Dihedral : 6.967 55.667 3216 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.41 % Allowed : 15.85 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.41 (0.15), residues: 2947 helix: -0.25 (0.24), residues: 497 sheet: 0.43 (0.16), residues: 931 loop : -0.68 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 226 HIS 0.006 0.001 HIS C 263 PHE 0.016 0.002 PHE B 493 TYR 0.014 0.002 TYR G 462 ARG 0.004 0.001 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 305 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.6903 (mt0) cc_final: 0.6658 (mm-40) REVERT: A 287 ARG cc_start: 0.5923 (mtt90) cc_final: 0.5021 (tmt170) REVERT: A 297 ARG cc_start: 0.4391 (OUTLIER) cc_final: 0.3980 (mmt90) REVERT: A 344 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.6737 (ttp80) REVERT: A 350 MET cc_start: 0.8525 (mmm) cc_final: 0.7648 (tmt) REVERT: A 403 GLN cc_start: 0.9533 (OUTLIER) cc_final: 0.8933 (mt0) REVERT: A 404 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.8885 (tp) REVERT: A 441 GLU cc_start: 0.8420 (tt0) cc_final: 0.7968 (tm-30) REVERT: A 447 GLN cc_start: 0.7383 (mt0) cc_final: 0.6950 (mp10) REVERT: A 465 GLU cc_start: 0.9035 (tt0) cc_final: 0.8694 (mm-30) REVERT: A 470 ARG cc_start: 0.9009 (mtt180) cc_final: 0.8416 (ptp90) REVERT: A 496 LYS cc_start: 0.7625 (tptm) cc_final: 0.7379 (tttm) REVERT: A 497 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7936 (p0) REVERT: A 541 GLN cc_start: 0.8371 (mt0) cc_final: 0.7891 (mt0) REVERT: A 560 GLN cc_start: 0.8653 (tp40) cc_final: 0.8200 (tp40) REVERT: A 579 ASP cc_start: 0.8690 (p0) cc_final: 0.8265 (t70) REVERT: A 586 LYS cc_start: 0.9122 (mttm) cc_final: 0.8784 (mtpp) REVERT: A 595 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7648 (mtm180) REVERT: B 287 ARG cc_start: 0.5932 (mtt90) cc_final: 0.5126 (ttp-170) REVERT: B 334 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6626 (pp) REVERT: B 344 ARG cc_start: 0.7322 (ttp-110) cc_final: 0.6353 (tmt170) REVERT: B 348 GLU cc_start: 0.8111 (tt0) cc_final: 0.7789 (pt0) REVERT: B 350 MET cc_start: 0.8305 (mmm) cc_final: 0.7606 (tmt) REVERT: B 387 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8372 (tmmt) REVERT: B 403 GLN cc_start: 0.9500 (OUTLIER) cc_final: 0.9153 (mt0) REVERT: B 404 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.8832 (tp) REVERT: B 441 GLU cc_start: 0.8308 (tt0) cc_final: 0.8093 (tt0) REVERT: B 447 GLN cc_start: 0.7551 (mt0) cc_final: 0.6968 (mp10) REVERT: B 465 GLU cc_start: 0.9040 (tt0) cc_final: 0.8636 (mm-30) REVERT: B 470 ARG cc_start: 0.8917 (mtt180) cc_final: 0.8559 (mtp-110) REVERT: B 541 GLN cc_start: 0.8271 (mt0) cc_final: 0.7721 (mt0) REVERT: B 557 GLN cc_start: 0.8567 (tp40) cc_final: 0.8256 (tp-100) REVERT: B 560 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8096 (tp40) REVERT: B 579 ASP cc_start: 0.8695 (p0) cc_final: 0.8226 (t0) REVERT: C 285 GLN cc_start: 0.6904 (mt0) cc_final: 0.6561 (mm-40) REVERT: C 287 ARG cc_start: 0.5768 (mtt90) cc_final: 0.4925 (ttp-110) REVERT: C 297 ARG cc_start: 0.4726 (OUTLIER) cc_final: 0.4302 (mmt90) REVERT: C 344 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.6827 (ttp80) REVERT: C 350 MET cc_start: 0.8411 (mmm) cc_final: 0.7517 (tmt) REVERT: C 404 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.8747 (tp) REVERT: C 441 GLU cc_start: 0.8519 (tt0) cc_final: 0.7932 (tm-30) REVERT: C 447 GLN cc_start: 0.7725 (mt0) cc_final: 0.7110 (mp10) REVERT: C 465 GLU cc_start: 0.9133 (tt0) cc_final: 0.8694 (mm-30) REVERT: C 470 ARG cc_start: 0.8829 (mtt180) cc_final: 0.8521 (ptm160) REVERT: C 496 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6842 (tptm) REVERT: C 539 ASN cc_start: 0.7314 (m110) cc_final: 0.6811 (m-40) REVERT: C 541 GLN cc_start: 0.8740 (mt0) cc_final: 0.8127 (mt0) REVERT: C 579 ASP cc_start: 0.8836 (p0) cc_final: 0.8546 (t0) REVERT: C 586 LYS cc_start: 0.9102 (mttm) cc_final: 0.8674 (mtpt) REVERT: D 180 ASN cc_start: 0.9350 (t0) cc_final: 0.8962 (t0) REVERT: D 285 GLN cc_start: 0.7105 (mt0) cc_final: 0.6760 (mm110) REVERT: D 287 ARG cc_start: 0.5703 (mtt90) cc_final: 0.4898 (ttp-110) REVERT: D 297 ARG cc_start: 0.5156 (OUTLIER) cc_final: 0.4854 (mmt90) REVERT: D 340 LEU cc_start: 0.7317 (mt) cc_final: 0.7085 (mm) REVERT: D 344 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.6743 (ttp-170) REVERT: D 398 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8851 (mp0) REVERT: D 403 GLN cc_start: 0.9476 (OUTLIER) cc_final: 0.8930 (mt0) REVERT: D 441 GLU cc_start: 0.8244 (tt0) cc_final: 0.7818 (tm-30) REVERT: D 447 GLN cc_start: 0.7340 (mt0) cc_final: 0.6855 (mp10) REVERT: D 557 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8139 (mp10) REVERT: D 579 ASP cc_start: 0.8745 (p0) cc_final: 0.8336 (t0) REVERT: E 209 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.6793 (p0) REVERT: E 285 GLN cc_start: 0.6604 (mt0) cc_final: 0.6342 (mm-40) REVERT: E 287 ARG cc_start: 0.5987 (mtt90) cc_final: 0.5227 (ttp-110) REVERT: E 344 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.6596 (ttp80) REVERT: E 348 GLU cc_start: 0.8062 (tt0) cc_final: 0.7729 (pt0) REVERT: E 350 MET cc_start: 0.8569 (mmm) cc_final: 0.7882 (ttp) REVERT: E 403 GLN cc_start: 0.9459 (OUTLIER) cc_final: 0.8880 (mt0) REVERT: E 404 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8658 (tp) REVERT: E 441 GLU cc_start: 0.8342 (tt0) cc_final: 0.7787 (tm-30) REVERT: E 447 GLN cc_start: 0.7480 (mt0) cc_final: 0.7023 (mp10) REVERT: E 465 GLU cc_start: 0.9126 (tt0) cc_final: 0.8785 (mm-30) REVERT: E 541 GLN cc_start: 0.8323 (mt0) cc_final: 0.7752 (mt0) REVERT: E 557 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8228 (tp-100) REVERT: E 579 ASP cc_start: 0.8843 (p0) cc_final: 0.8407 (t0) REVERT: F 209 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7126 (p0) REVERT: F 212 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8239 (mt-10) REVERT: F 285 GLN cc_start: 0.6721 (mt0) cc_final: 0.6361 (mm110) REVERT: F 330 SER cc_start: 0.4374 (m) cc_final: 0.3726 (p) REVERT: F 344 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6557 (ttp80) REVERT: F 350 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7666 (OUTLIER) REVERT: F 404 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8862 (tp) REVERT: F 441 GLU cc_start: 0.8548 (tt0) cc_final: 0.7960 (tm-30) REVERT: F 444 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7871 (mtpp) REVERT: F 447 GLN cc_start: 0.7361 (mt0) cc_final: 0.6898 (mp10) REVERT: F 465 GLU cc_start: 0.9168 (tt0) cc_final: 0.8644 (mm-30) REVERT: F 497 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7995 (p0) REVERT: F 557 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8676 (tm-30) REVERT: F 579 ASP cc_start: 0.8900 (p0) cc_final: 0.8457 (t0) REVERT: F 595 ARG cc_start: 0.7375 (mtm180) cc_final: 0.6838 (ptt-90) REVERT: G 271 LEU cc_start: 0.8777 (pt) cc_final: 0.8474 (pt) REVERT: G 285 GLN cc_start: 0.6768 (mt0) cc_final: 0.6537 (mm110) REVERT: G 287 ARG cc_start: 0.5968 (mtt90) cc_final: 0.5013 (ttp-170) REVERT: G 344 ARG cc_start: 0.7609 (ttp-110) cc_final: 0.6677 (tmt170) REVERT: G 350 MET cc_start: 0.8601 (mmm) cc_final: 0.7854 (ttp) REVERT: G 403 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8997 (mt0) REVERT: G 441 GLU cc_start: 0.8633 (tt0) cc_final: 0.8287 (mt-10) REVERT: G 447 GLN cc_start: 0.7322 (mt0) cc_final: 0.6985 (mp10) REVERT: G 448 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8460 (tp) REVERT: G 465 GLU cc_start: 0.9115 (tt0) cc_final: 0.8819 (mm-30) REVERT: G 541 GLN cc_start: 0.8408 (mt0) cc_final: 0.7819 (mt0) REVERT: G 555 ASP cc_start: 0.7953 (p0) cc_final: 0.7748 (p0) REVERT: G 557 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8239 (mp10) REVERT: G 579 ASP cc_start: 0.8688 (p0) cc_final: 0.8353 (t70) REVERT: G 587 MET cc_start: 0.9048 (mtt) cc_final: 0.8792 (mtm) outliers start: 142 outliers final: 74 residues processed: 394 average time/residue: 1.5596 time to fit residues: 690.9998 Evaluate side-chains 383 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 288 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 414 LYS Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 40.0000 chunk 201 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 254 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 476 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN C 476 ASN D 424 GLN D 476 ASN D 537 ASN D 541 GLN E 422 ASN E 424 GLN E 476 ASN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 476 ASN G 424 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 23709 Z= 0.412 Angle : 0.587 6.427 32228 Z= 0.312 Chirality : 0.049 0.168 3696 Planarity : 0.005 0.048 4249 Dihedral : 6.546 55.308 3202 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.75 % Allowed : 16.00 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.51 (0.15), residues: 2947 helix: -0.26 (0.24), residues: 497 sheet: 0.49 (0.16), residues: 931 loop : -0.86 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 226 HIS 0.007 0.001 HIS C 263 PHE 0.015 0.002 PHE B 493 TYR 0.014 0.002 TYR G 462 ARG 0.004 0.001 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 287 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.7096 (mt0) cc_final: 0.6811 (mm-40) REVERT: A 344 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.6721 (ttp80) REVERT: A 350 MET cc_start: 0.8547 (mmm) cc_final: 0.7669 (tmt) REVERT: A 403 GLN cc_start: 0.9527 (OUTLIER) cc_final: 0.8930 (mt0) REVERT: A 404 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.8883 (tp) REVERT: A 441 GLU cc_start: 0.8407 (tt0) cc_final: 0.8007 (tm-30) REVERT: A 447 GLN cc_start: 0.7377 (mt0) cc_final: 0.6962 (mp10) REVERT: A 465 GLU cc_start: 0.9097 (tt0) cc_final: 0.8689 (mm-30) REVERT: A 470 ARG cc_start: 0.9010 (mtt180) cc_final: 0.8414 (ptp90) REVERT: A 496 LYS cc_start: 0.7558 (tptm) cc_final: 0.7334 (tttp) REVERT: A 497 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7931 (p0) REVERT: A 541 GLN cc_start: 0.8416 (mt0) cc_final: 0.7970 (mt0) REVERT: A 557 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8295 (mp10) REVERT: A 560 GLN cc_start: 0.8628 (tp40) cc_final: 0.8198 (tp40) REVERT: A 579 ASP cc_start: 0.8691 (p0) cc_final: 0.8303 (t70) REVERT: A 586 LYS cc_start: 0.9092 (mttm) cc_final: 0.8584 (mtpt) REVERT: A 595 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7301 (ttp-110) REVERT: B 287 ARG cc_start: 0.5946 (mtt90) cc_final: 0.5194 (ttp-170) REVERT: B 334 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6452 (pp) REVERT: B 344 ARG cc_start: 0.7156 (ttp-110) cc_final: 0.6197 (tmt170) REVERT: B 348 GLU cc_start: 0.7966 (tt0) cc_final: 0.7675 (pt0) REVERT: B 350 MET cc_start: 0.8372 (mmm) cc_final: 0.7679 (tmt) REVERT: B 387 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8308 (ttpp) REVERT: B 403 GLN cc_start: 0.9500 (OUTLIER) cc_final: 0.8983 (mt0) REVERT: B 404 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.8839 (tp) REVERT: B 436 TYR cc_start: 0.8765 (t80) cc_final: 0.8560 (t80) REVERT: B 441 GLU cc_start: 0.8295 (tt0) cc_final: 0.8086 (tt0) REVERT: B 447 GLN cc_start: 0.7522 (mt0) cc_final: 0.6956 (mp10) REVERT: B 465 GLU cc_start: 0.9155 (tt0) cc_final: 0.8718 (mm-30) REVERT: B 470 ARG cc_start: 0.8928 (mtt180) cc_final: 0.8613 (mtp-110) REVERT: B 541 GLN cc_start: 0.8272 (mt0) cc_final: 0.7416 (mm-40) REVERT: B 543 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8371 (mm-40) REVERT: B 557 GLN cc_start: 0.8626 (tp40) cc_final: 0.8318 (tp-100) REVERT: B 560 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8070 (tp40) REVERT: B 579 ASP cc_start: 0.8680 (p0) cc_final: 0.8187 (t0) REVERT: C 285 GLN cc_start: 0.6882 (mt0) cc_final: 0.6633 (mm-40) REVERT: C 287 ARG cc_start: 0.5815 (mtt180) cc_final: 0.4938 (ttp-110) REVERT: C 344 ARG cc_start: 0.7500 (ttp-110) cc_final: 0.6797 (ttp80) REVERT: C 350 MET cc_start: 0.8415 (mmm) cc_final: 0.7501 (tmt) REVERT: C 404 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.8749 (tp) REVERT: C 441 GLU cc_start: 0.8459 (tt0) cc_final: 0.7964 (tm-30) REVERT: C 447 GLN cc_start: 0.7749 (mt0) cc_final: 0.7142 (mp10) REVERT: C 465 GLU cc_start: 0.9018 (tt0) cc_final: 0.8668 (mm-30) REVERT: C 470 ARG cc_start: 0.8822 (mtt180) cc_final: 0.8515 (ptm160) REVERT: C 539 ASN cc_start: 0.7229 (m110) cc_final: 0.6700 (m-40) REVERT: C 541 GLN cc_start: 0.8636 (mt0) cc_final: 0.8209 (mt0) REVERT: C 557 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8369 (mp10) REVERT: C 579 ASP cc_start: 0.8787 (p0) cc_final: 0.8460 (t0) REVERT: C 586 LYS cc_start: 0.9115 (mttm) cc_final: 0.8726 (mtpt) REVERT: C 587 MET cc_start: 0.8982 (mtt) cc_final: 0.8614 (mtp) REVERT: D 180 ASN cc_start: 0.9348 (t0) cc_final: 0.8944 (t0) REVERT: D 285 GLN cc_start: 0.7182 (mt0) cc_final: 0.6811 (mm110) REVERT: D 287 ARG cc_start: 0.5694 (mtt90) cc_final: 0.4903 (ttp-110) REVERT: D 340 LEU cc_start: 0.7377 (mt) cc_final: 0.7146 (mm) REVERT: D 344 ARG cc_start: 0.7376 (ttp-110) cc_final: 0.6556 (ttp-170) REVERT: D 398 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8863 (mp0) REVERT: D 403 GLN cc_start: 0.9475 (OUTLIER) cc_final: 0.8920 (mt0) REVERT: D 441 GLU cc_start: 0.8281 (tt0) cc_final: 0.7759 (tm-30) REVERT: D 447 GLN cc_start: 0.7362 (mt0) cc_final: 0.6854 (mp10) REVERT: D 465 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8539 (mm-30) REVERT: D 557 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8164 (mp10) REVERT: D 579 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8338 (t0) REVERT: E 285 GLN cc_start: 0.6557 (mt0) cc_final: 0.6331 (mm-40) REVERT: E 287 ARG cc_start: 0.5989 (mtt90) cc_final: 0.5155 (ttp-110) REVERT: E 344 ARG cc_start: 0.7481 (ttp-110) cc_final: 0.6565 (ttp80) REVERT: E 350 MET cc_start: 0.8573 (mmm) cc_final: 0.7896 (ttp) REVERT: E 403 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.8958 (mt0) REVERT: E 404 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8629 (tp) REVERT: E 441 GLU cc_start: 0.8346 (tt0) cc_final: 0.7790 (tm-30) REVERT: E 447 GLN cc_start: 0.7476 (mt0) cc_final: 0.6971 (mp10) REVERT: E 465 GLU cc_start: 0.9110 (tt0) cc_final: 0.8750 (mm-30) REVERT: E 557 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8103 (mp10) REVERT: E 579 ASP cc_start: 0.8916 (p0) cc_final: 0.8468 (t0) REVERT: F 209 ASN cc_start: 0.7789 (m-40) cc_final: 0.7279 (p0) REVERT: F 285 GLN cc_start: 0.6667 (mt0) cc_final: 0.6227 (mm110) REVERT: F 344 ARG cc_start: 0.7382 (ttp-110) cc_final: 0.6618 (ttp80) REVERT: F 350 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7691 (OUTLIER) REVERT: F 404 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8902 (tp) REVERT: F 441 GLU cc_start: 0.8517 (tt0) cc_final: 0.7904 (tm-30) REVERT: F 444 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7840 (mtpp) REVERT: F 447 GLN cc_start: 0.7403 (mt0) cc_final: 0.6927 (mp10) REVERT: F 465 GLU cc_start: 0.9140 (tt0) cc_final: 0.8683 (mm-30) REVERT: F 486 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8780 (mp0) REVERT: F 557 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8377 (mp10) REVERT: F 579 ASP cc_start: 0.8847 (p0) cc_final: 0.8369 (t0) REVERT: F 586 LYS cc_start: 0.9004 (mttm) cc_final: 0.8649 (mtpt) REVERT: F 595 ARG cc_start: 0.7489 (mtm180) cc_final: 0.6977 (ptt180) REVERT: G 271 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8429 (pt) REVERT: G 285 GLN cc_start: 0.6801 (mt0) cc_final: 0.6517 (mm-40) REVERT: G 287 ARG cc_start: 0.6002 (mtt90) cc_final: 0.5035 (ttp-170) REVERT: G 344 ARG cc_start: 0.7580 (ttp-110) cc_final: 0.6685 (tmt170) REVERT: G 350 MET cc_start: 0.8658 (mmm) cc_final: 0.7878 (ttp) REVERT: G 403 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.9020 (mt0) REVERT: G 441 GLU cc_start: 0.8641 (tt0) cc_final: 0.8288 (mt-10) REVERT: G 447 GLN cc_start: 0.7523 (mt0) cc_final: 0.7110 (mp10) REVERT: G 448 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8475 (tp) REVERT: G 465 GLU cc_start: 0.9108 (tt0) cc_final: 0.8776 (mm-30) REVERT: G 500 LEU cc_start: 0.9073 (mt) cc_final: 0.8865 (mm) REVERT: G 555 ASP cc_start: 0.7842 (p0) cc_final: 0.7619 (p0) REVERT: G 557 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8130 (mp10) REVERT: G 579 ASP cc_start: 0.8651 (p0) cc_final: 0.8296 (t0) REVERT: G 587 MET cc_start: 0.9072 (mtt) cc_final: 0.8850 (mtm) outliers start: 151 outliers final: 78 residues processed: 377 average time/residue: 1.4966 time to fit residues: 636.9784 Evaluate side-chains 372 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 276 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 276 ASP Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 346 TRP Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 414 LYS Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 211 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 476 ASN A 537 ASN A 541 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN D 424 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 GLN E 476 ASN F 268 ASN F 389 GLN F 422 ASN ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN G 424 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23709 Z= 0.190 Angle : 0.494 6.605 32228 Z= 0.262 Chirality : 0.045 0.168 3696 Planarity : 0.004 0.039 4249 Dihedral : 5.779 52.197 3196 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.70 % Allowed : 17.41 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.15), residues: 2947 helix: 0.18 (0.25), residues: 497 sheet: 0.92 (0.16), residues: 903 loop : -0.69 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 226 HIS 0.003 0.001 HIS C 263 PHE 0.013 0.001 PHE E 493 TYR 0.013 0.001 TYR C 411 ARG 0.002 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 299 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7922 (m-30) cc_final: 0.7522 (t0) REVERT: A 285 GLN cc_start: 0.7145 (mt0) cc_final: 0.6937 (mm-40) REVERT: A 344 ARG cc_start: 0.7458 (ttp-110) cc_final: 0.6606 (ttp80) REVERT: A 350 MET cc_start: 0.8358 (mmm) cc_final: 0.7428 (tmt) REVERT: A 403 GLN cc_start: 0.9480 (OUTLIER) cc_final: 0.8912 (mt0) REVERT: A 404 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8827 (tp) REVERT: A 441 GLU cc_start: 0.8377 (tt0) cc_final: 0.8131 (mt-10) REVERT: A 447 GLN cc_start: 0.7413 (mt0) cc_final: 0.7012 (mp10) REVERT: A 465 GLU cc_start: 0.9101 (tt0) cc_final: 0.8677 (mm-30) REVERT: A 470 ARG cc_start: 0.8999 (mtt180) cc_final: 0.8410 (ptp90) REVERT: A 541 GLN cc_start: 0.8316 (mt0) cc_final: 0.7939 (mt0) REVERT: A 557 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8333 (mp10) REVERT: A 560 GLN cc_start: 0.8625 (tp40) cc_final: 0.8148 (tp40) REVERT: A 579 ASP cc_start: 0.8769 (p0) cc_final: 0.8325 (t70) REVERT: A 586 LYS cc_start: 0.9129 (mttm) cc_final: 0.8617 (mtpt) REVERT: A 595 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7357 (ttp-110) REVERT: B 287 ARG cc_start: 0.5855 (mtt180) cc_final: 0.5080 (ttp-170) REVERT: B 344 ARG cc_start: 0.7315 (ttp-110) cc_final: 0.6371 (tmt170) REVERT: B 350 MET cc_start: 0.8309 (mmm) cc_final: 0.7666 (tmt) REVERT: B 387 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8107 (ttpp) REVERT: B 404 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8688 (tp) REVERT: B 447 GLN cc_start: 0.7495 (mt0) cc_final: 0.6927 (mp10) REVERT: B 465 GLU cc_start: 0.9169 (tt0) cc_final: 0.8706 (mm-30) REVERT: B 470 ARG cc_start: 0.8907 (mtt180) cc_final: 0.8592 (mtp-110) REVERT: B 541 GLN cc_start: 0.8332 (mt0) cc_final: 0.7504 (mm-40) REVERT: B 557 GLN cc_start: 0.8652 (tp40) cc_final: 0.8413 (mp10) REVERT: B 560 GLN cc_start: 0.8239 (tp-100) cc_final: 0.7986 (tp40) REVERT: B 579 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8203 (t0) REVERT: C 285 GLN cc_start: 0.6683 (mt0) cc_final: 0.6434 (mm-40) REVERT: C 287 ARG cc_start: 0.5762 (mtt180) cc_final: 0.4921 (ttp-110) REVERT: C 344 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.6808 (ttp80) REVERT: C 350 MET cc_start: 0.8311 (mmm) cc_final: 0.7393 (tmt) REVERT: C 404 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8733 (tp) REVERT: C 436 TYR cc_start: 0.8709 (t80) cc_final: 0.8494 (t80) REVERT: C 441 GLU cc_start: 0.8535 (tt0) cc_final: 0.8061 (mt-10) REVERT: C 447 GLN cc_start: 0.7718 (mt0) cc_final: 0.7120 (mp10) REVERT: C 465 GLU cc_start: 0.9083 (tt0) cc_final: 0.8712 (mm-30) REVERT: C 470 ARG cc_start: 0.8799 (mtt180) cc_final: 0.8498 (ptm160) REVERT: C 496 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6900 (tptm) REVERT: C 539 ASN cc_start: 0.7207 (m110) cc_final: 0.6849 (m-40) REVERT: C 541 GLN cc_start: 0.8548 (mt0) cc_final: 0.8154 (mt0) REVERT: C 557 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8352 (mp10) REVERT: C 579 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8511 (t0) REVERT: C 586 LYS cc_start: 0.9050 (mttm) cc_final: 0.8728 (mtpt) REVERT: C 587 MET cc_start: 0.8849 (mtt) cc_final: 0.8425 (mtp) REVERT: D 180 ASN cc_start: 0.9311 (t0) cc_final: 0.8916 (t0) REVERT: D 285 GLN cc_start: 0.7192 (mt0) cc_final: 0.6923 (mm110) REVERT: D 287 ARG cc_start: 0.5601 (mtt90) cc_final: 0.4833 (ttp-110) REVERT: D 297 ARG cc_start: 0.4849 (OUTLIER) cc_final: 0.4478 (mmt90) REVERT: D 344 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.6694 (ttp-170) REVERT: D 398 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8862 (mp0) REVERT: D 403 GLN cc_start: 0.9465 (OUTLIER) cc_final: 0.8933 (mt0) REVERT: D 404 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8822 (tp) REVERT: D 441 GLU cc_start: 0.8279 (tt0) cc_final: 0.7723 (tm-30) REVERT: D 447 GLN cc_start: 0.7319 (mt0) cc_final: 0.6837 (mp10) REVERT: D 465 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8459 (mm-30) REVERT: D 557 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8184 (mp10) REVERT: D 579 ASP cc_start: 0.8952 (p0) cc_final: 0.8456 (t0) REVERT: D 595 ARG cc_start: 0.7886 (mtm180) cc_final: 0.7457 (ptt-90) REVERT: E 285 GLN cc_start: 0.6535 (mt0) cc_final: 0.6301 (mm-40) REVERT: E 287 ARG cc_start: 0.5849 (mtt180) cc_final: 0.5131 (ttp-110) REVERT: E 344 ARG cc_start: 0.7405 (ttp-110) cc_final: 0.6545 (ttp80) REVERT: E 350 MET cc_start: 0.8475 (mmm) cc_final: 0.7863 (ttp) REVERT: E 403 GLN cc_start: 0.9479 (OUTLIER) cc_final: 0.8882 (mt0) REVERT: E 404 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8635 (tp) REVERT: E 441 GLU cc_start: 0.8396 (tt0) cc_final: 0.7728 (tm-30) REVERT: E 444 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7773 (ptmt) REVERT: E 446 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8241 (mmtm) REVERT: E 447 GLN cc_start: 0.7336 (mt0) cc_final: 0.6817 (mp10) REVERT: E 465 GLU cc_start: 0.9060 (tt0) cc_final: 0.8722 (mm-30) REVERT: E 557 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8055 (mp10) REVERT: E 579 ASP cc_start: 0.8816 (p0) cc_final: 0.8352 (t0) REVERT: E 586 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8907 (mtpt) REVERT: F 271 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8349 (pp) REVERT: F 285 GLN cc_start: 0.6566 (mt0) cc_final: 0.6185 (mm110) REVERT: F 344 ARG cc_start: 0.7314 (ttp-110) cc_final: 0.6520 (ttp80) REVERT: F 350 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7608 (tmt) REVERT: F 404 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8823 (tp) REVERT: F 441 GLU cc_start: 0.8550 (tt0) cc_final: 0.7953 (mm-30) REVERT: F 444 LYS cc_start: 0.8399 (mtmt) cc_final: 0.8054 (mtpp) REVERT: F 447 GLN cc_start: 0.7338 (mt0) cc_final: 0.6933 (mp10) REVERT: F 465 GLU cc_start: 0.9158 (tt0) cc_final: 0.8706 (mm-30) REVERT: F 557 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8427 (mp10) REVERT: F 579 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8361 (t0) REVERT: F 595 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7412 (ptt-90) REVERT: G 180 ASN cc_start: 0.9291 (t0) cc_final: 0.8969 (t0) REVERT: G 271 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8421 (pt) REVERT: G 285 GLN cc_start: 0.6711 (mt0) cc_final: 0.6446 (mm-40) REVERT: G 287 ARG cc_start: 0.5916 (mtt90) cc_final: 0.4862 (ttp-170) REVERT: G 344 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.6714 (ttp80) REVERT: G 350 MET cc_start: 0.8557 (mmm) cc_final: 0.8155 (mmt) REVERT: G 403 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8982 (mt0) REVERT: G 404 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8736 (tp) REVERT: G 441 GLU cc_start: 0.8576 (tt0) cc_final: 0.8262 (mt-10) REVERT: G 447 GLN cc_start: 0.7464 (mt0) cc_final: 0.7132 (mp10) REVERT: G 465 GLU cc_start: 0.9143 (tt0) cc_final: 0.8758 (mm-30) REVERT: G 500 LEU cc_start: 0.9121 (mt) cc_final: 0.8884 (mm) REVERT: G 557 GLN cc_start: 0.8488 (tp-100) cc_final: 0.8217 (mp10) REVERT: G 579 ASP cc_start: 0.8753 (p0) cc_final: 0.8345 (t0) REVERT: G 587 MET cc_start: 0.8914 (mtt) cc_final: 0.8660 (mtm) outliers start: 97 outliers final: 43 residues processed: 343 average time/residue: 1.5575 time to fit residues: 600.0236 Evaluate side-chains 347 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 283 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain E residue 346 TRP Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 579 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 577 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 236 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 424 GLN A 476 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN D 424 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 ASN E 424 GLN E 499 ASN E 570 ASN F 422 ASN ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23709 Z= 0.193 Angle : 0.490 6.375 32228 Z= 0.259 Chirality : 0.045 0.159 3696 Planarity : 0.004 0.037 4249 Dihedral : 5.468 49.420 3183 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.30 % Allowed : 17.56 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.15), residues: 2947 helix: 0.32 (0.26), residues: 497 sheet: 1.03 (0.16), residues: 903 loop : -0.64 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 226 HIS 0.002 0.001 HIS D 299 PHE 0.012 0.001 PHE B 493 TYR 0.013 0.001 TYR C 411 ARG 0.002 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 288 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7884 (m-30) cc_final: 0.7499 (t0) REVERT: A 344 ARG cc_start: 0.7543 (ttp-110) cc_final: 0.6695 (ttp80) REVERT: A 350 MET cc_start: 0.8351 (mmm) cc_final: 0.7399 (tmt) REVERT: A 403 GLN cc_start: 0.9472 (OUTLIER) cc_final: 0.8885 (mt0) REVERT: A 404 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.8809 (tp) REVERT: A 441 GLU cc_start: 0.8354 (tt0) cc_final: 0.8100 (mt-10) REVERT: A 447 GLN cc_start: 0.7407 (mt0) cc_final: 0.6993 (mp10) REVERT: A 465 GLU cc_start: 0.9091 (tt0) cc_final: 0.8673 (mm-30) REVERT: A 470 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8417 (ptp90) REVERT: A 541 GLN cc_start: 0.8339 (mt0) cc_final: 0.7949 (mt0) REVERT: A 557 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8405 (mp10) REVERT: A 560 GLN cc_start: 0.8602 (tp40) cc_final: 0.8090 (tp40) REVERT: A 570 ASN cc_start: 0.8951 (m-40) cc_final: 0.8618 (p0) REVERT: A 579 ASP cc_start: 0.8797 (p0) cc_final: 0.8347 (t70) REVERT: A 586 LYS cc_start: 0.9144 (mttm) cc_final: 0.8728 (mtpt) REVERT: A 595 ARG cc_start: 0.7771 (mtm180) cc_final: 0.7355 (ttp-110) REVERT: B 180 ASN cc_start: 0.9255 (t0) cc_final: 0.8863 (t0) REVERT: B 287 ARG cc_start: 0.5898 (mtt180) cc_final: 0.5114 (ttp-170) REVERT: B 344 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.6478 (tmt170) REVERT: B 350 MET cc_start: 0.8270 (mmm) cc_final: 0.7653 (tmt) REVERT: B 387 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8103 (ttpp) REVERT: B 404 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8680 (tp) REVERT: B 447 GLN cc_start: 0.7497 (mt0) cc_final: 0.6931 (mp10) REVERT: B 465 GLU cc_start: 0.9138 (tt0) cc_final: 0.8705 (mm-30) REVERT: B 541 GLN cc_start: 0.8379 (mt0) cc_final: 0.7539 (mm-40) REVERT: B 557 GLN cc_start: 0.8655 (tp40) cc_final: 0.8428 (mp10) REVERT: B 560 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7994 (tp40) REVERT: B 579 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8299 (t0) REVERT: C 285 GLN cc_start: 0.6665 (mt0) cc_final: 0.6411 (mm-40) REVERT: C 287 ARG cc_start: 0.5793 (mtt180) cc_final: 0.4946 (ttp-110) REVERT: C 344 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.6749 (ttp80) REVERT: C 350 MET cc_start: 0.8287 (mmm) cc_final: 0.7339 (tmt) REVERT: C 404 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8728 (tp) REVERT: C 436 TYR cc_start: 0.8721 (t80) cc_final: 0.8488 (t80) REVERT: C 441 GLU cc_start: 0.8543 (tt0) cc_final: 0.8078 (mt-10) REVERT: C 447 GLN cc_start: 0.7700 (mt0) cc_final: 0.7109 (mp10) REVERT: C 465 GLU cc_start: 0.9110 (tt0) cc_final: 0.8684 (mm-30) REVERT: C 470 ARG cc_start: 0.8811 (mtt180) cc_final: 0.8467 (ptm160) REVERT: C 496 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6878 (tptm) REVERT: C 539 ASN cc_start: 0.7059 (m110) cc_final: 0.6525 (m-40) REVERT: C 541 GLN cc_start: 0.8560 (mt0) cc_final: 0.8183 (mt0) REVERT: C 557 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8375 (mp10) REVERT: C 579 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8519 (t0) REVERT: C 586 LYS cc_start: 0.9038 (mttm) cc_final: 0.8698 (mtpt) REVERT: C 587 MET cc_start: 0.8804 (mtt) cc_final: 0.8434 (mtp) REVERT: D 180 ASN cc_start: 0.9262 (t0) cc_final: 0.8864 (t0) REVERT: D 285 GLN cc_start: 0.7048 (mt0) cc_final: 0.6750 (mm110) REVERT: D 287 ARG cc_start: 0.5623 (mtt180) cc_final: 0.4852 (ttp-110) REVERT: D 297 ARG cc_start: 0.4853 (OUTLIER) cc_final: 0.4485 (mmt90) REVERT: D 344 ARG cc_start: 0.7423 (ttp-110) cc_final: 0.6707 (ttp-170) REVERT: D 398 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8874 (mp0) REVERT: D 403 GLN cc_start: 0.9452 (OUTLIER) cc_final: 0.9004 (mt0) REVERT: D 404 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8808 (tp) REVERT: D 441 GLU cc_start: 0.8279 (tt0) cc_final: 0.7741 (tm-30) REVERT: D 447 GLN cc_start: 0.7273 (mt0) cc_final: 0.6840 (mp10) REVERT: D 465 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8481 (mm-30) REVERT: D 557 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8195 (mp10) REVERT: D 579 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8383 (t0) REVERT: E 285 GLN cc_start: 0.6476 (mt0) cc_final: 0.6237 (mm-40) REVERT: E 335 ASP cc_start: 0.7298 (m-30) cc_final: 0.6521 (t0) REVERT: E 344 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6436 (ttp80) REVERT: E 350 MET cc_start: 0.8456 (mmm) cc_final: 0.7851 (ttp) REVERT: E 403 GLN cc_start: 0.9480 (OUTLIER) cc_final: 0.8878 (mt0) REVERT: E 404 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.8630 (tp) REVERT: E 441 GLU cc_start: 0.8402 (tt0) cc_final: 0.7691 (tm-30) REVERT: E 444 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7790 (ptmt) REVERT: E 446 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8206 (mmtm) REVERT: E 447 GLN cc_start: 0.7304 (mt0) cc_final: 0.6783 (mp10) REVERT: E 465 GLU cc_start: 0.9075 (tt0) cc_final: 0.8754 (mm-30) REVERT: E 557 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8102 (mp10) REVERT: E 579 ASP cc_start: 0.8762 (p0) cc_final: 0.8308 (t0) REVERT: E 586 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8715 (mtpt) REVERT: F 209 ASN cc_start: 0.7575 (m-40) cc_final: 0.6866 (p0) REVERT: F 271 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8390 (pp) REVERT: F 285 GLN cc_start: 0.6694 (mt0) cc_final: 0.6345 (mm110) REVERT: F 344 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.6495 (ttp80) REVERT: F 350 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7592 (tmt) REVERT: F 404 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8779 (tp) REVERT: F 441 GLU cc_start: 0.8498 (tt0) cc_final: 0.7922 (mm-30) REVERT: F 444 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8085 (mtpp) REVERT: F 447 GLN cc_start: 0.7309 (mt0) cc_final: 0.6831 (mp10) REVERT: F 465 GLU cc_start: 0.9157 (tt0) cc_final: 0.8705 (mm-30) REVERT: F 486 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8867 (mp0) REVERT: F 557 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8470 (mp10) REVERT: F 579 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8290 (t0) REVERT: F 586 LYS cc_start: 0.9006 (mttm) cc_final: 0.8608 (mtpt) REVERT: F 595 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7355 (ptt-90) REVERT: G 180 ASN cc_start: 0.9302 (t0) cc_final: 0.8965 (t0) REVERT: G 271 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8442 (pt) REVERT: G 285 GLN cc_start: 0.6566 (mt0) cc_final: 0.6330 (mm-40) REVERT: G 287 ARG cc_start: 0.5906 (mtt90) cc_final: 0.4875 (ttp-170) REVERT: G 344 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.6692 (ttp80) REVERT: G 350 MET cc_start: 0.8518 (mmm) cc_final: 0.7826 (ttp) REVERT: G 403 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8988 (mt0) REVERT: G 404 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8723 (tp) REVERT: G 441 GLU cc_start: 0.8553 (tt0) cc_final: 0.8263 (mt-10) REVERT: G 447 GLN cc_start: 0.7523 (mt0) cc_final: 0.7181 (mp10) REVERT: G 448 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8475 (tp) REVERT: G 465 GLU cc_start: 0.9077 (tt0) cc_final: 0.8640 (mm-30) REVERT: G 500 LEU cc_start: 0.9118 (mt) cc_final: 0.8880 (mm) REVERT: G 557 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8292 (mp10) REVERT: G 579 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8301 (t0) REVERT: G 587 MET cc_start: 0.8905 (mtt) cc_final: 0.8675 (mtm) outliers start: 113 outliers final: 57 residues processed: 343 average time/residue: 1.5255 time to fit residues: 588.9658 Evaluate side-chains 364 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 282 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 346 TRP Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 579 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 394 ILE Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Chi-restraints excluded: chain G residue 579 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN C 476 ASN D 424 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN G 424 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 23709 Z= 0.361 Angle : 0.558 9.017 32228 Z= 0.294 Chirality : 0.048 0.177 3696 Planarity : 0.005 0.043 4249 Dihedral : 5.787 52.793 3182 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.88 % Allowed : 17.45 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.15), residues: 2947 helix: 0.10 (0.25), residues: 497 sheet: 0.74 (0.15), residues: 959 loop : -0.69 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 226 HIS 0.005 0.001 HIS C 263 PHE 0.014 0.002 PHE B 493 TYR 0.013 0.002 TYR C 411 ARG 0.004 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 271 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7832 (m-30) cc_final: 0.7485 (t0) REVERT: A 287 ARG cc_start: 0.5753 (mtt90) cc_final: 0.4913 (tmt170) REVERT: A 344 ARG cc_start: 0.7523 (ttp-110) cc_final: 0.6759 (ttp-170) REVERT: A 348 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: A 350 MET cc_start: 0.8572 (mmm) cc_final: 0.7757 (tmt) REVERT: A 403 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.8897 (mt0) REVERT: A 404 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.8880 (tp) REVERT: A 441 GLU cc_start: 0.8439 (tt0) cc_final: 0.8163 (mt-10) REVERT: A 447 GLN cc_start: 0.7439 (mt0) cc_final: 0.6990 (mp10) REVERT: A 465 GLU cc_start: 0.9063 (tt0) cc_final: 0.8702 (mm-30) REVERT: A 470 ARG cc_start: 0.9016 (mtt180) cc_final: 0.8416 (ptp90) REVERT: A 541 GLN cc_start: 0.8364 (mt0) cc_final: 0.7971 (mt0) REVERT: A 557 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8401 (mp10) REVERT: A 560 GLN cc_start: 0.8659 (tp40) cc_final: 0.8184 (tp40) REVERT: A 570 ASN cc_start: 0.8779 (m-40) cc_final: 0.8575 (p0) REVERT: A 579 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8330 (t70) REVERT: A 586 LYS cc_start: 0.9119 (mttm) cc_final: 0.8647 (mtpt) REVERT: A 595 ARG cc_start: 0.7664 (mtm180) cc_final: 0.7240 (ttp-110) REVERT: B 287 ARG cc_start: 0.6042 (mtt180) cc_final: 0.5258 (ttp-170) REVERT: B 335 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6404 (t0) REVERT: B 344 ARG cc_start: 0.7438 (ttp-110) cc_final: 0.6464 (tmt170) REVERT: B 350 MET cc_start: 0.8317 (mmm) cc_final: 0.7646 (tmt) REVERT: B 404 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8773 (tp) REVERT: B 447 GLN cc_start: 0.7519 (mt0) cc_final: 0.6948 (mp10) REVERT: B 465 GLU cc_start: 0.9054 (tt0) cc_final: 0.8728 (mm-30) REVERT: B 470 ARG cc_start: 0.8997 (ttm170) cc_final: 0.8596 (mtp-110) REVERT: B 541 GLN cc_start: 0.8416 (mt0) cc_final: 0.7513 (mm-40) REVERT: B 557 GLN cc_start: 0.8675 (tp40) cc_final: 0.8426 (mp10) REVERT: B 560 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7974 (tp40) REVERT: B 579 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8291 (t0) REVERT: C 285 GLN cc_start: 0.6723 (mt0) cc_final: 0.6440 (mm-40) REVERT: C 287 ARG cc_start: 0.5878 (mtt180) cc_final: 0.5002 (ttp-110) REVERT: C 344 ARG cc_start: 0.7435 (ttp-110) cc_final: 0.6701 (ttp80) REVERT: C 350 MET cc_start: 0.8391 (mmm) cc_final: 0.7472 (tmt) REVERT: C 404 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8729 (tp) REVERT: C 441 GLU cc_start: 0.8468 (tt0) cc_final: 0.7968 (tm-30) REVERT: C 447 GLN cc_start: 0.7728 (mt0) cc_final: 0.7155 (mp10) REVERT: C 465 GLU cc_start: 0.9115 (tt0) cc_final: 0.8730 (mm-30) REVERT: C 470 ARG cc_start: 0.8744 (mtt180) cc_final: 0.8486 (ptm160) REVERT: C 496 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6902 (tptm) REVERT: C 541 GLN cc_start: 0.8444 (mt0) cc_final: 0.7721 (mm-40) REVERT: C 557 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8405 (mp10) REVERT: C 579 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8474 (t0) REVERT: C 586 LYS cc_start: 0.9081 (mttm) cc_final: 0.8740 (mtpt) REVERT: C 587 MET cc_start: 0.8956 (mtt) cc_final: 0.8547 (mtp) REVERT: D 180 ASN cc_start: 0.9313 (t0) cc_final: 0.8930 (t0) REVERT: D 285 GLN cc_start: 0.6915 (mt0) cc_final: 0.6627 (mm-40) REVERT: D 287 ARG cc_start: 0.5799 (mtt180) cc_final: 0.4967 (ttp-110) REVERT: D 297 ARG cc_start: 0.4783 (OUTLIER) cc_final: 0.4474 (mmt90) REVERT: D 344 ARG cc_start: 0.7375 (ttp-110) cc_final: 0.6577 (ttp-170) REVERT: D 398 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8858 (mp0) REVERT: D 403 GLN cc_start: 0.9501 (OUTLIER) cc_final: 0.8989 (mt0) REVERT: D 441 GLU cc_start: 0.8213 (tt0) cc_final: 0.7706 (tm-30) REVERT: D 447 GLN cc_start: 0.7309 (mt0) cc_final: 0.6876 (mp10) REVERT: D 465 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8430 (mm-30) REVERT: D 557 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8179 (mp10) REVERT: D 579 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8355 (t0) REVERT: E 285 GLN cc_start: 0.6561 (mt0) cc_final: 0.6334 (mm-40) REVERT: E 287 ARG cc_start: 0.6027 (mtt180) cc_final: 0.5167 (ttp-110) REVERT: E 344 ARG cc_start: 0.7311 (ttp-110) cc_final: 0.6434 (ttp80) REVERT: E 348 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: E 350 MET cc_start: 0.8590 (mmm) cc_final: 0.8067 (ttp) REVERT: E 403 GLN cc_start: 0.9504 (OUTLIER) cc_final: 0.8954 (mt0) REVERT: E 404 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8600 (tp) REVERT: E 441 GLU cc_start: 0.8333 (tt0) cc_final: 0.7738 (tm-30) REVERT: E 447 GLN cc_start: 0.7328 (mt0) cc_final: 0.6986 (mp10) REVERT: E 465 GLU cc_start: 0.9074 (tt0) cc_final: 0.8776 (mm-30) REVERT: E 557 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8058 (mp10) REVERT: E 579 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8286 (t0) REVERT: F 250 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8873 (pm20) REVERT: F 271 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8442 (pp) REVERT: F 285 GLN cc_start: 0.6683 (mt0) cc_final: 0.6306 (mm110) REVERT: F 287 ARG cc_start: 0.6112 (mtt180) cc_final: 0.5027 (tmt170) REVERT: F 297 ARG cc_start: 0.4699 (OUTLIER) cc_final: 0.4229 (mmt90) REVERT: F 344 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.6625 (ttp80) REVERT: F 350 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7616 (tmt) REVERT: F 389 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: F 404 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8835 (tp) REVERT: F 441 GLU cc_start: 0.8547 (tt0) cc_final: 0.7994 (tm-30) REVERT: F 444 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8086 (mtpp) REVERT: F 447 GLN cc_start: 0.7439 (mt0) cc_final: 0.6924 (mp10) REVERT: F 465 GLU cc_start: 0.9148 (tt0) cc_final: 0.8727 (mm-30) REVERT: F 486 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8896 (mp0) REVERT: F 557 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8455 (mp10) REVERT: F 579 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8372 (t0) REVERT: F 586 LYS cc_start: 0.9040 (mttm) cc_final: 0.8687 (mtpt) REVERT: F 595 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7235 (ptt180) REVERT: G 271 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8449 (pt) REVERT: G 285 GLN cc_start: 0.6809 (mt0) cc_final: 0.6571 (mm-40) REVERT: G 287 ARG cc_start: 0.5997 (mtt180) cc_final: 0.4916 (ttp-170) REVERT: G 344 ARG cc_start: 0.7479 (ttp-110) cc_final: 0.6650 (ttp80) REVERT: G 350 MET cc_start: 0.8644 (mmm) cc_final: 0.7875 (ttp) REVERT: G 403 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.9000 (mt0) REVERT: G 404 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.8797 (tp) REVERT: G 441 GLU cc_start: 0.8575 (tt0) cc_final: 0.8290 (mt-10) REVERT: G 447 GLN cc_start: 0.7485 (mt0) cc_final: 0.7136 (mp10) REVERT: G 448 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8473 (tp) REVERT: G 465 GLU cc_start: 0.9090 (tt0) cc_final: 0.8683 (mm-30) REVERT: G 557 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8248 (mp10) REVERT: G 579 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8309 (t0) REVERT: G 587 MET cc_start: 0.9035 (mtt) cc_final: 0.8818 (mtm) outliers start: 128 outliers final: 77 residues processed: 338 average time/residue: 1.5838 time to fit residues: 600.8252 Evaluate side-chains 373 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 266 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 346 TRP Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 486 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 579 ASP Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 579 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Chi-restraints excluded: chain G residue 579 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 54 optimal weight: 40.0000 chunk 180 optimal weight: 20.0000 chunk 193 optimal weight: 3.9990 chunk 140 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 222 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN C 476 ASN D 424 GLN E 422 ASN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN G 424 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 23709 Z= 0.399 Angle : 0.578 9.889 32228 Z= 0.305 Chirality : 0.048 0.170 3696 Planarity : 0.005 0.046 4249 Dihedral : 5.907 55.175 3182 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.07 % Allowed : 17.41 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.25 (0.15), residues: 2947 helix: -0.02 (0.24), residues: 497 sheet: 0.71 (0.15), residues: 945 loop : -0.76 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 226 HIS 0.005 0.001 HIS C 263 PHE 0.015 0.002 PHE B 493 TYR 0.014 0.002 TYR G 462 ARG 0.004 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 261 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7856 (m-30) cc_final: 0.7501 (t0) REVERT: A 344 ARG cc_start: 0.7535 (ttp-110) cc_final: 0.6680 (ttp80) REVERT: A 348 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: A 350 MET cc_start: 0.8605 (mmm) cc_final: 0.7779 (tmt) REVERT: A 403 GLN cc_start: 0.9530 (OUTLIER) cc_final: 0.8932 (mt0) REVERT: A 404 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.8876 (tp) REVERT: A 441 GLU cc_start: 0.8470 (tt0) cc_final: 0.8018 (tm-30) REVERT: A 447 GLN cc_start: 0.7461 (mt0) cc_final: 0.7026 (mp10) REVERT: A 465 GLU cc_start: 0.9079 (tt0) cc_final: 0.8711 (mm-30) REVERT: A 470 ARG cc_start: 0.9007 (mtt180) cc_final: 0.8413 (ptp90) REVERT: A 560 GLN cc_start: 0.8574 (tp40) cc_final: 0.8162 (tp40) REVERT: A 579 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8308 (t70) REVERT: A 586 LYS cc_start: 0.9143 (mttm) cc_final: 0.8818 (mtpp) REVERT: B 287 ARG cc_start: 0.6094 (mtt180) cc_final: 0.5300 (ttp-170) REVERT: B 335 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6344 (t0) REVERT: B 344 ARG cc_start: 0.7497 (ttp-110) cc_final: 0.6581 (ttp80) REVERT: B 348 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: B 350 MET cc_start: 0.8362 (mmm) cc_final: 0.7661 (tmt) REVERT: B 404 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8814 (tp) REVERT: B 447 GLN cc_start: 0.7523 (mt0) cc_final: 0.6968 (mp10) REVERT: B 465 GLU cc_start: 0.9066 (tt0) cc_final: 0.8746 (mm-30) REVERT: B 541 GLN cc_start: 0.8434 (mt0) cc_final: 0.7537 (mm-40) REVERT: B 557 GLN cc_start: 0.8677 (tp40) cc_final: 0.8426 (mp10) REVERT: B 560 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7978 (tp40) REVERT: B 579 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8265 (t0) REVERT: C 285 GLN cc_start: 0.6870 (mt0) cc_final: 0.6602 (mm-40) REVERT: C 287 ARG cc_start: 0.5910 (mtt180) cc_final: 0.5021 (ttp-110) REVERT: C 344 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.6690 (ttp80) REVERT: C 350 MET cc_start: 0.8416 (mmm) cc_final: 0.7501 (tmt) REVERT: C 404 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8720 (tp) REVERT: C 436 TYR cc_start: 0.8744 (t80) cc_final: 0.8489 (t80) REVERT: C 441 GLU cc_start: 0.8462 (tt0) cc_final: 0.7967 (tm-30) REVERT: C 447 GLN cc_start: 0.7663 (mt0) cc_final: 0.7093 (mp10) REVERT: C 465 GLU cc_start: 0.9083 (tt0) cc_final: 0.8735 (mm-30) REVERT: C 470 ARG cc_start: 0.8752 (mtt180) cc_final: 0.8496 (ptm160) REVERT: C 496 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6896 (tptm) REVERT: C 512 ASP cc_start: 0.8908 (t0) cc_final: 0.8666 (t0) REVERT: C 541 GLN cc_start: 0.8479 (mt0) cc_final: 0.7788 (mm-40) REVERT: C 557 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8398 (mp10) REVERT: C 579 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8393 (t0) REVERT: C 586 LYS cc_start: 0.9118 (mttm) cc_final: 0.8733 (mtpt) REVERT: C 587 MET cc_start: 0.9016 (mtt) cc_final: 0.8677 (mtp) REVERT: D 180 ASN cc_start: 0.9327 (t0) cc_final: 0.8920 (t0) REVERT: D 285 GLN cc_start: 0.7088 (mt0) cc_final: 0.6859 (mm-40) REVERT: D 287 ARG cc_start: 0.5921 (mtt180) cc_final: 0.5050 (ttp-110) REVERT: D 297 ARG cc_start: 0.5144 (OUTLIER) cc_final: 0.4785 (mmt90) REVERT: D 344 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.6605 (ttp-170) REVERT: D 398 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8856 (mp0) REVERT: D 403 GLN cc_start: 0.9480 (OUTLIER) cc_final: 0.8926 (mt0) REVERT: D 441 GLU cc_start: 0.8211 (tt0) cc_final: 0.7737 (tm-30) REVERT: D 447 GLN cc_start: 0.7388 (mt0) cc_final: 0.6972 (mp10) REVERT: D 465 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8449 (mm-30) REVERT: D 557 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8176 (mp10) REVERT: D 579 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8306 (t0) REVERT: E 285 GLN cc_start: 0.6645 (mt0) cc_final: 0.6381 (mm-40) REVERT: E 287 ARG cc_start: 0.6059 (mtt180) cc_final: 0.5192 (ttp-110) REVERT: E 344 ARG cc_start: 0.7335 (ttp-110) cc_final: 0.6459 (ttp80) REVERT: E 348 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: E 350 MET cc_start: 0.8586 (mmm) cc_final: 0.8044 (ttp) REVERT: E 403 GLN cc_start: 0.9492 (OUTLIER) cc_final: 0.8926 (mt0) REVERT: E 404 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8603 (tp) REVERT: E 441 GLU cc_start: 0.8319 (tt0) cc_final: 0.7736 (tm-30) REVERT: E 447 GLN cc_start: 0.7248 (mt0) cc_final: 0.6884 (mp10) REVERT: E 465 GLU cc_start: 0.9054 (tt0) cc_final: 0.8851 (mm-30) REVERT: E 557 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8061 (mp10) REVERT: E 579 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8273 (t0) REVERT: F 209 ASN cc_start: 0.7565 (m-40) cc_final: 0.6888 (p0) REVERT: F 285 GLN cc_start: 0.6717 (mt0) cc_final: 0.6340 (mm110) REVERT: F 287 ARG cc_start: 0.6219 (mtt180) cc_final: 0.5078 (tmt170) REVERT: F 297 ARG cc_start: 0.4553 (OUTLIER) cc_final: 0.4093 (mmt90) REVERT: F 344 ARG cc_start: 0.7462 (ttp-110) cc_final: 0.6632 (ttp80) REVERT: F 350 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7616 (tmt) REVERT: F 389 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: F 404 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.8864 (tp) REVERT: F 441 GLU cc_start: 0.8498 (tt0) cc_final: 0.7982 (tm-30) REVERT: F 447 GLN cc_start: 0.7440 (mt0) cc_final: 0.6928 (mp10) REVERT: F 465 GLU cc_start: 0.9064 (tt0) cc_final: 0.8716 (mm-30) REVERT: F 486 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8848 (mp0) REVERT: F 557 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8461 (mp10) REVERT: F 579 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8379 (t0) REVERT: F 586 LYS cc_start: 0.9019 (mttm) cc_final: 0.8628 (mtpt) REVERT: F 595 ARG cc_start: 0.7702 (mtm180) cc_final: 0.7211 (ptt180) REVERT: G 271 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8378 (pt) REVERT: G 285 GLN cc_start: 0.6824 (mt0) cc_final: 0.6587 (mm-40) REVERT: G 287 ARG cc_start: 0.6028 (mtt180) cc_final: 0.4935 (ttp-170) REVERT: G 344 ARG cc_start: 0.7292 (ttp-110) cc_final: 0.6621 (ttp-170) REVERT: G 350 MET cc_start: 0.8684 (mmm) cc_final: 0.7901 (ttp) REVERT: G 403 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8962 (mt0) REVERT: G 434 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8293 (ttp) REVERT: G 441 GLU cc_start: 0.8584 (tt0) cc_final: 0.8308 (mt-10) REVERT: G 447 GLN cc_start: 0.7630 (mt0) cc_final: 0.7140 (mp10) REVERT: G 448 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8467 (tp) REVERT: G 465 GLU cc_start: 0.9091 (tt0) cc_final: 0.8696 (mm-30) REVERT: G 557 GLN cc_start: 0.8505 (tp-100) cc_final: 0.8242 (mp10) REVERT: G 560 GLN cc_start: 0.8469 (tp40) cc_final: 0.8228 (tp40) REVERT: G 579 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8326 (t0) REVERT: G 587 MET cc_start: 0.9040 (mtt) cc_final: 0.8799 (mtm) outliers start: 133 outliers final: 81 residues processed: 332 average time/residue: 1.5621 time to fit residues: 583.9899 Evaluate side-chains 367 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 257 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 346 TRP Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 579 ASP Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 579 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Chi-restraints excluded: chain G residue 579 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 264 optimal weight: 30.0000 chunk 158 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 476 ASN C 476 ASN D 424 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23709 Z= 0.401 Angle : 0.585 10.946 32228 Z= 0.308 Chirality : 0.049 0.169 3696 Planarity : 0.005 0.045 4249 Dihedral : 5.894 54.406 3182 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.91 % Allowed : 17.68 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.32 (0.15), residues: 2947 helix: -0.03 (0.24), residues: 497 sheet: 0.63 (0.15), residues: 945 loop : -0.79 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 226 HIS 0.005 0.001 HIS C 263 PHE 0.015 0.002 PHE B 493 TYR 0.014 0.002 TYR G 462 ARG 0.004 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 261 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7860 (m-30) cc_final: 0.7503 (t0) REVERT: A 344 ARG cc_start: 0.7527 (ttp-110) cc_final: 0.6755 (ttp-170) REVERT: A 348 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: A 350 MET cc_start: 0.8610 (mmm) cc_final: 0.7781 (tmt) REVERT: A 403 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.8931 (mt0) REVERT: A 404 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.8875 (tp) REVERT: A 441 GLU cc_start: 0.8470 (tt0) cc_final: 0.8033 (tm-30) REVERT: A 447 GLN cc_start: 0.7451 (mt0) cc_final: 0.7026 (mp10) REVERT: A 465 GLU cc_start: 0.9077 (tt0) cc_final: 0.8714 (mm-30) REVERT: A 470 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8412 (ptp90) REVERT: A 560 GLN cc_start: 0.8559 (tp40) cc_final: 0.8111 (tp40) REVERT: A 579 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8309 (t70) REVERT: A 586 LYS cc_start: 0.9155 (mttm) cc_final: 0.8842 (mtpp) REVERT: B 287 ARG cc_start: 0.6099 (mtt180) cc_final: 0.5301 (ttp-170) REVERT: B 335 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6400 (t0) REVERT: B 344 ARG cc_start: 0.7492 (ttp-110) cc_final: 0.6581 (ttp80) REVERT: B 348 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: B 350 MET cc_start: 0.8371 (mmm) cc_final: 0.7663 (tmt) REVERT: B 404 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.8819 (tp) REVERT: B 447 GLN cc_start: 0.7557 (mt0) cc_final: 0.7031 (mp10) REVERT: B 465 GLU cc_start: 0.9074 (tt0) cc_final: 0.8764 (mm-30) REVERT: B 541 GLN cc_start: 0.8436 (mt0) cc_final: 0.7544 (mm-40) REVERT: B 557 GLN cc_start: 0.8676 (tp40) cc_final: 0.8427 (mp10) REVERT: B 560 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7973 (tp40) REVERT: B 579 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8278 (t0) REVERT: C 285 GLN cc_start: 0.6901 (mt0) cc_final: 0.6642 (mm-40) REVERT: C 287 ARG cc_start: 0.5930 (mtt180) cc_final: 0.5038 (ttp-110) REVERT: C 344 ARG cc_start: 0.7454 (ttp-110) cc_final: 0.6774 (ttp80) REVERT: C 350 MET cc_start: 0.8436 (mmm) cc_final: 0.7471 (tmt) REVERT: C 404 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8718 (tp) REVERT: C 434 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8323 (ttp) REVERT: C 436 TYR cc_start: 0.8678 (t80) cc_final: 0.8428 (t80) REVERT: C 441 GLU cc_start: 0.8455 (tt0) cc_final: 0.7990 (tm-30) REVERT: C 447 GLN cc_start: 0.7665 (mt0) cc_final: 0.7097 (mp10) REVERT: C 465 GLU cc_start: 0.9085 (tt0) cc_final: 0.8741 (mm-30) REVERT: C 470 ARG cc_start: 0.8751 (mtt180) cc_final: 0.8498 (ptm160) REVERT: C 496 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6904 (tptm) REVERT: C 512 ASP cc_start: 0.8904 (t0) cc_final: 0.8663 (t0) REVERT: C 541 GLN cc_start: 0.8511 (mt0) cc_final: 0.7828 (mm-40) REVERT: C 557 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8396 (mp10) REVERT: C 579 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8391 (t0) REVERT: C 586 LYS cc_start: 0.9105 (mttm) cc_final: 0.8719 (mtpt) REVERT: C 587 MET cc_start: 0.9025 (mtt) cc_final: 0.8682 (mtp) REVERT: D 180 ASN cc_start: 0.9332 (t0) cc_final: 0.8919 (t0) REVERT: D 285 GLN cc_start: 0.7062 (mt0) cc_final: 0.6812 (mm-40) REVERT: D 287 ARG cc_start: 0.5864 (mtt180) cc_final: 0.5027 (ttp-110) REVERT: D 297 ARG cc_start: 0.5154 (OUTLIER) cc_final: 0.4796 (mmt90) REVERT: D 344 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.6626 (ttp-170) REVERT: D 398 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8853 (mp0) REVERT: D 403 GLN cc_start: 0.9483 (OUTLIER) cc_final: 0.8949 (mt0) REVERT: D 441 GLU cc_start: 0.8208 (tt0) cc_final: 0.7737 (tm-30) REVERT: D 447 GLN cc_start: 0.7433 (mt0) cc_final: 0.6991 (mp10) REVERT: D 465 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8432 (mm-30) REVERT: D 557 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8185 (mp10) REVERT: D 579 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8298 (t0) REVERT: E 285 GLN cc_start: 0.6679 (mt0) cc_final: 0.6424 (mm-40) REVERT: E 287 ARG cc_start: 0.6004 (mtt180) cc_final: 0.5152 (ttp-110) REVERT: E 344 ARG cc_start: 0.7420 (ttp-110) cc_final: 0.6513 (ttp80) REVERT: E 348 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: E 350 MET cc_start: 0.8591 (mmm) cc_final: 0.8048 (ttp) REVERT: E 403 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.8952 (mt0) REVERT: E 404 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8633 (tp) REVERT: E 441 GLU cc_start: 0.8322 (tt0) cc_final: 0.7769 (tm-30) REVERT: E 447 GLN cc_start: 0.7257 (mt0) cc_final: 0.6895 (mp10) REVERT: E 465 GLU cc_start: 0.9051 (tt0) cc_final: 0.8849 (mm-30) REVERT: E 557 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8070 (mp10) REVERT: E 579 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8275 (t0) REVERT: F 209 ASN cc_start: 0.7559 (m-40) cc_final: 0.6880 (p0) REVERT: F 271 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8450 (pp) REVERT: F 285 GLN cc_start: 0.6753 (mt0) cc_final: 0.6350 (mm110) REVERT: F 287 ARG cc_start: 0.6223 (mtt180) cc_final: 0.5089 (tmt170) REVERT: F 297 ARG cc_start: 0.4551 (OUTLIER) cc_final: 0.4091 (mmt90) REVERT: F 344 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.6640 (ttp80) REVERT: F 350 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7621 (tmt) REVERT: F 389 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: F 404 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.8897 (tp) REVERT: F 441 GLU cc_start: 0.8485 (tt0) cc_final: 0.7983 (tm-30) REVERT: F 447 GLN cc_start: 0.7449 (mt0) cc_final: 0.6930 (mp10) REVERT: F 465 GLU cc_start: 0.9042 (tt0) cc_final: 0.8677 (mm-30) REVERT: F 486 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8844 (mp0) REVERT: F 557 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8485 (mp10) REVERT: F 579 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8355 (t0) REVERT: F 586 LYS cc_start: 0.9021 (mttm) cc_final: 0.8627 (mtpt) REVERT: G 271 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8404 (pt) REVERT: G 285 GLN cc_start: 0.6887 (mt0) cc_final: 0.6653 (mm-40) REVERT: G 287 ARG cc_start: 0.6046 (mtt180) cc_final: 0.4948 (ttp-170) REVERT: G 344 ARG cc_start: 0.7278 (ttp-110) cc_final: 0.6496 (ttp80) REVERT: G 350 MET cc_start: 0.8700 (mmm) cc_final: 0.7662 (pp-130) REVERT: G 403 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.8994 (mt0) REVERT: G 441 GLU cc_start: 0.8583 (tt0) cc_final: 0.8278 (mt-10) REVERT: G 447 GLN cc_start: 0.7633 (mt0) cc_final: 0.7144 (mp10) REVERT: G 448 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8481 (tt) REVERT: G 465 GLU cc_start: 0.9065 (tt0) cc_final: 0.8656 (mm-30) REVERT: G 560 GLN cc_start: 0.8439 (tp40) cc_final: 0.8200 (tp40) REVERT: G 579 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8344 (t0) REVERT: G 587 MET cc_start: 0.9043 (mtt) cc_final: 0.8793 (mtm) outliers start: 129 outliers final: 82 residues processed: 329 average time/residue: 1.5401 time to fit residues: 571.4749 Evaluate side-chains 371 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 259 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 346 TRP Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 579 ASP Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 579 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Chi-restraints excluded: chain G residue 579 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 292 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 561 ASN A 584 ASN B 476 ASN C 476 ASN D 424 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 23709 Z= 0.345 Angle : 0.567 11.414 32228 Z= 0.298 Chirality : 0.047 0.165 3696 Planarity : 0.005 0.044 4249 Dihedral : 5.804 54.683 3182 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.50 % Allowed : 18.40 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.28 (0.15), residues: 2947 helix: 0.04 (0.25), residues: 497 sheet: 0.63 (0.15), residues: 945 loop : -0.77 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 226 HIS 0.004 0.001 HIS C 263 PHE 0.014 0.002 PHE B 493 TYR 0.013 0.002 TYR G 462 ARG 0.003 0.000 ARG B 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 263 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 ASP cc_start: 0.7846 (m-30) cc_final: 0.7497 (t0) REVERT: A 344 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.6805 (ttp-170) REVERT: A 350 MET cc_start: 0.8588 (mmm) cc_final: 0.7768 (tmt) REVERT: A 403 GLN cc_start: 0.9513 (OUTLIER) cc_final: 0.8903 (mt0) REVERT: A 404 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.8874 (tp) REVERT: A 441 GLU cc_start: 0.8489 (tt0) cc_final: 0.7995 (tm-30) REVERT: A 447 GLN cc_start: 0.7458 (mt0) cc_final: 0.7042 (mp10) REVERT: A 465 GLU cc_start: 0.9068 (tt0) cc_final: 0.8673 (mm-30) REVERT: A 470 ARG cc_start: 0.9013 (mtt180) cc_final: 0.8417 (ptp90) REVERT: A 560 GLN cc_start: 0.8633 (tp40) cc_final: 0.8165 (tp40) REVERT: A 579 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8307 (t70) REVERT: A 586 LYS cc_start: 0.9188 (mttm) cc_final: 0.8782 (mtpt) REVERT: B 287 ARG cc_start: 0.6080 (mtt180) cc_final: 0.5274 (ttp-170) REVERT: B 335 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6351 (t0) REVERT: B 344 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.6595 (ttp80) REVERT: B 350 MET cc_start: 0.8351 (mmm) cc_final: 0.7659 (tmt) REVERT: B 404 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8771 (tp) REVERT: B 447 GLN cc_start: 0.7556 (mt0) cc_final: 0.7038 (mp10) REVERT: B 465 GLU cc_start: 0.9077 (tt0) cc_final: 0.8754 (mm-30) REVERT: B 541 GLN cc_start: 0.8437 (mt0) cc_final: 0.7548 (mm-40) REVERT: B 557 GLN cc_start: 0.8668 (tp40) cc_final: 0.8430 (mp10) REVERT: B 560 GLN cc_start: 0.8253 (tp-100) cc_final: 0.8052 (tp40) REVERT: B 579 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8283 (t0) REVERT: C 285 GLN cc_start: 0.6883 (mt0) cc_final: 0.6637 (mm-40) REVERT: C 287 ARG cc_start: 0.5927 (mtt180) cc_final: 0.5039 (ttp-110) REVERT: C 344 ARG cc_start: 0.7441 (ttp-110) cc_final: 0.6726 (ttp80) REVERT: C 350 MET cc_start: 0.8430 (mmm) cc_final: 0.7463 (tmt) REVERT: C 404 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8721 (tp) REVERT: C 436 TYR cc_start: 0.8659 (t80) cc_final: 0.8409 (t80) REVERT: C 441 GLU cc_start: 0.8459 (tt0) cc_final: 0.7984 (tm-30) REVERT: C 447 GLN cc_start: 0.7684 (mt0) cc_final: 0.7126 (mp10) REVERT: C 465 GLU cc_start: 0.9086 (tt0) cc_final: 0.8735 (mm-30) REVERT: C 470 ARG cc_start: 0.8842 (mtt180) cc_final: 0.8491 (ptm160) REVERT: C 496 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6898 (tptm) REVERT: C 512 ASP cc_start: 0.8897 (t0) cc_final: 0.8656 (t0) REVERT: C 541 GLN cc_start: 0.8401 (mt0) cc_final: 0.7694 (mm-40) REVERT: C 557 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8402 (mp10) REVERT: C 579 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8395 (t0) REVERT: C 586 LYS cc_start: 0.9106 (mttm) cc_final: 0.8725 (mtpt) REVERT: C 587 MET cc_start: 0.9002 (mtt) cc_final: 0.8602 (mtp) REVERT: D 180 ASN cc_start: 0.9321 (t0) cc_final: 0.8912 (t0) REVERT: D 285 GLN cc_start: 0.7132 (mt0) cc_final: 0.6906 (mm-40) REVERT: D 287 ARG cc_start: 0.5926 (mtt180) cc_final: 0.4979 (tmt170) REVERT: D 297 ARG cc_start: 0.5136 (OUTLIER) cc_final: 0.4782 (mmt90) REVERT: D 344 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.6608 (ttp-170) REVERT: D 398 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8843 (mp0) REVERT: D 403 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.8934 (mt0) REVERT: D 441 GLU cc_start: 0.8204 (tt0) cc_final: 0.7708 (tm-30) REVERT: D 447 GLN cc_start: 0.7427 (mt0) cc_final: 0.6988 (mp10) REVERT: D 465 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8507 (mm-30) REVERT: D 521 MET cc_start: 0.8745 (tpt) cc_final: 0.8532 (tpt) REVERT: D 557 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8180 (mp10) REVERT: D 579 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8298 (t0) REVERT: E 285 GLN cc_start: 0.6716 (mt0) cc_final: 0.6454 (mm-40) REVERT: E 287 ARG cc_start: 0.6030 (mtt180) cc_final: 0.5219 (ttp-110) REVERT: E 344 ARG cc_start: 0.7450 (ttp-110) cc_final: 0.6492 (ttp80) REVERT: E 348 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: E 350 MET cc_start: 0.8586 (mmm) cc_final: 0.8040 (ttp) REVERT: E 403 GLN cc_start: 0.9484 (OUTLIER) cc_final: 0.8917 (mt0) REVERT: E 404 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8603 (tp) REVERT: E 441 GLU cc_start: 0.8350 (tt0) cc_final: 0.7735 (tm-30) REVERT: E 447 GLN cc_start: 0.7263 (mt0) cc_final: 0.6888 (mp10) REVERT: E 465 GLU cc_start: 0.9043 (tt0) cc_final: 0.8836 (mm-30) REVERT: E 557 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8074 (mp10) REVERT: E 579 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8278 (t0) REVERT: F 209 ASN cc_start: 0.7560 (m-40) cc_final: 0.6888 (p0) REVERT: F 271 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8431 (pp) REVERT: F 285 GLN cc_start: 0.6915 (mt0) cc_final: 0.6625 (mm110) REVERT: F 287 ARG cc_start: 0.6200 (mtt180) cc_final: 0.5078 (tmt170) REVERT: F 297 ARG cc_start: 0.4696 (OUTLIER) cc_final: 0.4229 (mmt90) REVERT: F 344 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.6625 (ttp80) REVERT: F 350 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7615 (tmt) REVERT: F 389 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: F 404 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8846 (tp) REVERT: F 441 GLU cc_start: 0.8481 (tt0) cc_final: 0.7978 (tm-30) REVERT: F 447 GLN cc_start: 0.7438 (mt0) cc_final: 0.6923 (mp10) REVERT: F 465 GLU cc_start: 0.9047 (tt0) cc_final: 0.8705 (mm-30) REVERT: F 486 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8844 (mp0) REVERT: F 557 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8487 (mp10) REVERT: F 579 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8364 (t0) REVERT: F 586 LYS cc_start: 0.9007 (mttm) cc_final: 0.8609 (mtpt) REVERT: F 595 ARG cc_start: 0.7758 (mpp80) cc_final: 0.7449 (ptt-90) REVERT: G 180 ASN cc_start: 0.9319 (t0) cc_final: 0.8993 (t0) REVERT: G 271 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8453 (pt) REVERT: G 285 GLN cc_start: 0.6995 (mt0) cc_final: 0.6765 (mm-40) REVERT: G 287 ARG cc_start: 0.6030 (mtt180) cc_final: 0.4937 (ttp-170) REVERT: G 344 ARG cc_start: 0.7216 (ttp-110) cc_final: 0.6434 (ttp80) REVERT: G 350 MET cc_start: 0.8692 (mmm) cc_final: 0.7898 (ttp) REVERT: G 403 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.8961 (mt0) REVERT: G 404 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.8794 (tp) REVERT: G 441 GLU cc_start: 0.8619 (tt0) cc_final: 0.8313 (mt-10) REVERT: G 447 GLN cc_start: 0.7681 (mt0) cc_final: 0.7211 (mp10) REVERT: G 448 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8527 (tp) REVERT: G 465 GLU cc_start: 0.9082 (tt0) cc_final: 0.8697 (mm-30) REVERT: G 560 GLN cc_start: 0.8401 (tp40) cc_final: 0.8180 (tp40) REVERT: G 579 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8331 (t0) REVERT: G 587 MET cc_start: 0.9017 (mtt) cc_final: 0.8809 (mtm) outliers start: 118 outliers final: 76 residues processed: 324 average time/residue: 1.5355 time to fit residues: 563.2119 Evaluate side-chains 363 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 259 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 511 SER Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 346 TRP Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 403 GLN Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 446 LYS Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 579 ASP Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 346 TRP Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 433 THR Chi-restraints excluded: chain F residue 486 GLU Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 579 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 486 GLU Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 577 VAL Chi-restraints excluded: chain G residue 579 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 239 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 424 GLN A 476 ASN B 198 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN G 424 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104169 restraints weight = 32500.155| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.78 r_work: 0.3127 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23709 Z= 0.155 Angle : 0.496 10.002 32228 Z= 0.259 Chirality : 0.044 0.160 3696 Planarity : 0.004 0.036 4249 Dihedral : 5.337 49.872 3182 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.20 % Allowed : 19.70 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.12 (0.15), residues: 2947 helix: 0.47 (0.26), residues: 497 sheet: 1.04 (0.16), residues: 889 loop : -0.61 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 226 HIS 0.002 0.000 HIS E 299 PHE 0.012 0.001 PHE B 493 TYR 0.012 0.001 TYR C 411 ARG 0.002 0.000 ARG B 468 =============================================================================== Job complete usr+sys time: 9721.27 seconds wall clock time: 172 minutes 24.68 seconds (10344.68 seconds total)