Starting phenix.real_space_refine (version: dev) on Thu Dec 15 16:56:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/12_2022/3j9c_6224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/12_2022/3j9c_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_6224/12_2022/3j9c_6224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/12_2022/3j9c_6224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/12_2022/3j9c_6224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/12_2022/3j9c_6224.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B GLU 212": "OE1" <-> "OE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A 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" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H GLU 515": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 26624 Number of models: 1 Model: "" Number of chains: 8 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: "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: "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 " Chain: "H" 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 H 596 " pdbres=" CA H 801 " Not linked: pdbres=" CA H 801 " pdbres=" CA H 802 " Time building chain proxies: 14.23, per 1000 atoms: 0.53 Number of scatterers: 26624 At special positions: 0 Unit cell: (143.36, 140.8, 244.48, 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 16 19.99 S 40 16.00 O 5368 8.00 N 4624 7.00 C 16576 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: 9.79 Conformation dependent library (CDL) restraints added in 4.1 seconds 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 72 sheets defined 20.8% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 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: 3.689A 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: 3.775A 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: 3.568A 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: 3.690A 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: 3.774A 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: 3.610A 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: 3.567A pdb=" N THR C 576 " --> pdb=" O ASN C 573 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.689A 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: 3.821A 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: 3.568A 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: 3.690A 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: 3.775A 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: 3.862A 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: 3.689A 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: 3.774A 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: 3.567A 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: 3.690A 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: 3.775A 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 helix chain 'H' and resid 184 through 191 Processing helix chain 'H' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU H 212 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 241 Processing helix chain 'H' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS H 253 " --> pdb=" O GLU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 446 Processing helix chain 'H' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL H 480 " --> pdb=" O ASN H 476 " (cutoff:3.500A) Proline residue: H 482 - end of helix Processing helix chain 'H' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS H 518 " --> pdb=" O GLU H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 532 Processing helix chain 'H' and resid 555 through 569 Processing helix chain 'H' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR H 576 " --> pdb=" O ASN H 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU H 578 " --> pdb=" O TYR H 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: 4.320A 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: 4.796A 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: 4.772A 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: 3.773A pdb=" N GLN B 454 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 6.938A 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: 6.628A 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: 6.833A 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: 7.017A pdb=" N VAL C 367 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 5.518A 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: 3.800A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 4.321A 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: 4.773A 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: 6.937A 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: 8.445A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.629A 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: 5.519A 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: 4.797A 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: 5.138A pdb=" N ASN D 458 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D 454 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 6.938A 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: 6.627A 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: 6.832A 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: 3.799A 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: 6.681A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.859A 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: 5.139A pdb=" N ASN E 458 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 3.773A 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: 6.833A 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: 7.016A 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: 7.009A 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: 6.682A 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: 6.858A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.772A 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: 6.937A 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: 6.628A 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: 6.832A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.134A 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: 7.017A pdb=" N VAL G 367 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET G 266 " --> pdb=" O ARG G 365 " (cutoff:3.500A) removed outlier: 7.010A 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: 4.320A 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: 6.681A 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: 6.859A 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: 7.120A pdb=" N VAL G 384 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 5.491A 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: 8.444A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.627A 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: 8.133A 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 Processing sheet with id= 64, first strand: chain 'H' and resid 192 through 196 Processing sheet with id= 65, first strand: chain 'H' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL H 264 " --> pdb=" O VAL H 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL H 367 " --> pdb=" O VAL H 264 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N MET H 266 " --> pdb=" O ARG H 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG H 365 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN H 268 " --> pdb=" O ASN H 363 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'H' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN H 409 " --> pdb=" O ASN H 368 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE H 432 " --> pdb=" O LEU H 360 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'H' and resid 276 through 299 Processing sheet with id= 68, first strand: chain 'H' and resid 302 through 311 Processing sheet with id= 69, first strand: chain 'H' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU H 383 " --> pdb=" O LEU H 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR H 393 " --> pdb=" O THR H 381 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR H 381 " --> pdb=" O THR H 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS H 395 " --> pdb=" O PRO H 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN H 376 " --> pdb=" O ASN H 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN H 458 " --> pdb=" O ASN H 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN H 454 " --> pdb=" O THR H 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER H 382 " --> pdb=" O THR H 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR H 452 " --> pdb=" O SER H 382 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL H 384 " --> pdb=" O LEU H 450 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU H 450 " --> pdb=" O VAL H 384 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'H' and resid 460 through 462 Processing sheet with id= 71, first strand: chain 'H' and resid 501 through 506 removed outlier: 8.445A pdb=" N ILE H 589 " --> pdb=" O THR H 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG H 490 " --> pdb=" O ILE H 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE H 591 " --> pdb=" O ARG H 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE H 492 " --> pdb=" O ILE H 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP H 593 " --> pdb=" O ILE H 492 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'H' and resid 541 through 542 920 hydrogen bonds defined for protein. 2496 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: 9.30 Time building geometry restraints manager: 10.69 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: 8875 1.34 - 1.45: 3279 1.45 - 1.57: 14854 1.57 - 1.69: 8 1.69 - 1.81: 80 Bond restraints: 27096 Sorted by residual: bond pdb=" CA LYS G 444 " pdb=" C LYS G 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 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 3.75e+01 bond pdb=" CA LYS F 444 " pdb=" C LYS F 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 H 444 " pdb=" C LYS H 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 B 444 " pdb=" C LYS B 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.73e+01 ... (remaining 27091 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.16: 705 106.16 - 113.12: 14737 113.12 - 120.07: 8581 120.07 - 127.03: 12647 127.03 - 133.98: 162 Bond angle restraints: 36832 Sorted by residual: angle pdb=" C ALA B 417 " pdb=" N PRO B 418 " pdb=" CA PRO B 418 " ideal model delta sigma weight residual 119.78 125.41 -5.63 1.03e+00 9.43e-01 2.99e+01 angle pdb=" C ALA H 417 " pdb=" N PRO H 418 " pdb=" CA PRO H 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 2.97e+01 angle pdb=" C ALA D 417 " pdb=" N PRO D 418 " pdb=" CA PRO D 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 ... (remaining 36827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.73: 14571 13.73 - 27.45: 1221 27.45 - 41.17: 432 41.17 - 54.90: 216 54.90 - 68.62: 96 Dihedral angle restraints: 16536 sinusoidal: 6592 harmonic: 9944 Sorted by residual: dihedral pdb=" CA SER E 413 " pdb=" C SER E 413 " pdb=" N LYS E 414 " pdb=" CA LYS E 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 H 413 " pdb=" C SER H 413 " pdb=" N LYS H 414 " pdb=" CA LYS H 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 16533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3316 0.050 - 0.100: 697 0.100 - 0.151: 187 0.151 - 0.201: 8 0.201 - 0.251: 16 Chirality restraints: 4224 Sorted by residual: chirality pdb=" CA LYS B 444 " pdb=" N LYS B 444 " pdb=" C LYS B 444 " pdb=" CB LYS B 444 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA LYS F 444 " pdb=" N LYS F 444 " pdb=" C LYS F 444 " pdb=" CB LYS F 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 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 1.55e+00 ... (remaining 4221 not shown) Planarity restraints: 4856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 378 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.02e+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 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 C 378 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO C 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 379 " 0.024 5.00e-02 4.00e+02 ... (remaining 4853 not shown) Histogram of nonbonded interaction distances: 0.25 - 1.18: 180 1.18 - 2.11: 825 2.11 - 3.04: 17706 3.04 - 3.97: 75639 3.97 - 4.90: 143544 Warning: very small nonbonded interaction distances. Nonbonded interactions: 237894 Sorted by model distance: nonbonded pdb=" O LYS B 397 " pdb=" CE3 TRP F 346 " model vdw 0.248 3.340 nonbonded pdb=" CE3 TRP B 346 " pdb=" O LYS F 397 " model vdw 0.248 3.340 nonbonded pdb=" CB THR B 354 " pdb=" C THR D 433 " model vdw 0.262 3.700 nonbonded pdb=" C THR B 433 " pdb=" CB THR D 354 " model vdw 0.262 3.700 nonbonded pdb=" CA ASN B 435 " pdb=" CA ASN D 435 " model vdw 0.397 3.900 ... (remaining 237889 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' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 16 9.91 5 S 40 5.16 5 C 16576 2.51 5 N 4624 2.21 5 O 5368 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.170 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: 3.540 Check model and map are aligned: 0.400 Convert atoms to be neutral: 0.220 Process input model: 66.080 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 27096 Z= 0.355 Angle : 1.112 10.831 36832 Z= 0.743 Chirality : 0.047 0.251 4224 Planarity : 0.004 0.043 4856 Dihedral : 14.410 68.624 10072 Min Nonbonded Distance : 0.248 Molprobity Statistics. All-atom Clashscore : 26.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 6.13 % 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: -0.81 (0.15), residues: 3368 helix: -1.67 (0.19), residues: 568 sheet: -0.98 (0.14), residues: 1144 loop : 0.51 (0.17), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 608 time to evaluate : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 184 outliers final: 27 residues processed: 735 average time/residue: 1.3378 time to fit residues: 1140.8181 Evaluate side-chains 362 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 335 time to evaluate : 3.332 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 27 residues processed: 4 average time/residue: 0.7730 time to fit residues: 8.3083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 263 optimal weight: 40.0000 chunk 101 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 305 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 HIS ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN A 424 GLN A 483 GLN A 499 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN C 274 ASN C 483 GLN C 557 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 499 ASN ** E 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 274 ASN F 285 GLN F 389 GLN ** F 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN F 483 GLN F 557 GLN F 570 ASN G 209 ASN G 274 ASN G 389 GLN ** G 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 483 GLN G 499 ASN H 209 ASN H 274 ASN H 285 GLN ** H 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 424 GLN H 483 GLN H 560 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.363 27096 Z= 0.668 Angle : 1.149 29.397 36832 Z= 0.647 Chirality : 0.063 0.634 4224 Planarity : 0.007 0.147 4856 Dihedral : 6.927 51.060 3616 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 29.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer Outliers : 5.63 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.68 % 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: -0.39 (0.14), residues: 3368 helix: -0.36 (0.25), residues: 480 sheet: 0.05 (0.15), residues: 1000 loop : -0.30 (0.15), residues: 1888 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 331 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 79 residues processed: 450 average time/residue: 1.3868 time to fit residues: 722.7274 Evaluate side-chains 358 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 279 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 60 residues processed: 19 average time/residue: 0.3679 time to fit residues: 15.5697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 253 optimal weight: 0.4980 chunk 207 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 330 optimal weight: 6.9990 chunk 272 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN A 424 GLN A 476 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN C 476 ASN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 ASN D 541 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN ** F 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN F 476 ASN F 570 ASN G 389 GLN H 198 ASN H 285 GLN H 424 GLN ** H 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.236 27096 Z= 0.482 Angle : 0.931 24.120 36832 Z= 0.520 Chirality : 0.057 0.602 4224 Planarity : 0.006 0.126 4856 Dihedral : 6.536 49.066 3616 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 24.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.13 % Favored : 95.75 % Rotamer Outliers : 5.40 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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 (0.14), residues: 3368 helix: -0.04 (0.24), residues: 536 sheet: 0.48 (0.16), residues: 960 loop : -0.59 (0.14), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 290 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 83 residues processed: 412 average time/residue: 1.3546 time to fit residues: 648.5959 Evaluate side-chains 349 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 266 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 60 residues processed: 24 average time/residue: 0.6552 time to fit residues: 25.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.5980 chunk 229 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 33 optimal weight: 0.0970 chunk 145 optimal weight: 0.7980 chunk 205 optimal weight: 6.9990 chunk 306 optimal weight: 20.0000 chunk 324 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN C 198 ASN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 ASN E 541 GLN F 277 GLN F 280 GLN F 285 GLN ** F 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 424 GLN H 537 ASN H 541 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.239 27096 Z= 0.364 Angle : 0.826 24.994 36832 Z= 0.464 Chirality : 0.053 0.876 4224 Planarity : 0.005 0.114 4856 Dihedral : 6.221 54.578 3616 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer Outliers : 4.47 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.68 % 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: 0.08 (0.15), residues: 3368 helix: 0.40 (0.25), residues: 560 sheet: 1.20 (0.17), residues: 872 loop : -0.59 (0.14), residues: 1936 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 297 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 70 residues processed: 403 average time/residue: 1.2554 time to fit residues: 595.3396 Evaluate side-chains 328 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 258 time to evaluate : 3.176 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 54 residues processed: 18 average time/residue: 1.0175 time to fit residues: 26.3434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 4 optimal weight: 50.0000 chunk 241 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 277 optimal weight: 0.6980 chunk 224 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 165 optimal weight: 10.0000 chunk 291 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN A 422 ASN A 424 GLN A 476 ASN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN D 476 ASN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 GLN E 476 ASN F 280 GLN F 285 GLN F 424 GLN F 476 ASN ** G 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 539 ASN G 560 GLN ** H 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.234 27096 Z= 0.409 Angle : 0.836 28.022 36832 Z= 0.469 Chirality : 0.054 0.939 4224 Planarity : 0.005 0.108 4856 Dihedral : 6.348 59.267 3616 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer Outliers : 5.27 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.81 % 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: -0.04 (0.14), residues: 3368 helix: 0.37 (0.24), residues: 552 sheet: 1.16 (0.17), residues: 856 loop : -0.69 (0.14), residues: 1960 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 270 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 158 outliers final: 95 residues processed: 379 average time/residue: 1.3328 time to fit residues: 589.0411 Evaluate side-chains 348 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 253 time to evaluate : 3.296 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 62 residues processed: 33 average time/residue: 0.4845 time to fit residues: 27.1188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.9980 chunk 292 optimal weight: 0.0770 chunk 64 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 27 optimal weight: 40.0000 chunk 107 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 overall best weight: 1.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN ** G 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 539 ASN G 560 GLN ** H 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.245 27096 Z= 0.366 Angle : 0.807 29.514 36832 Z= 0.456 Chirality : 0.053 0.907 4224 Planarity : 0.005 0.096 4856 Dihedral : 6.125 64.217 3616 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer Outliers : 4.47 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.84 % 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: 0.08 (0.15), residues: 3368 helix: 0.47 (0.25), residues: 568 sheet: 1.35 (0.16), residues: 856 loop : -0.68 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 267 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 82 residues processed: 363 average time/residue: 1.3036 time to fit residues: 553.8237 Evaluate side-chains 327 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 245 time to evaluate : 3.082 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 61 residues processed: 22 average time/residue: 0.6327 time to fit residues: 22.7510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 183 optimal weight: 50.0000 chunk 273 optimal weight: 0.0980 chunk 181 optimal weight: 20.0000 chunk 323 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 476 ASN C 422 ASN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN D 476 ASN ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 280 GLN F 424 GLN ** G 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN ** H 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.252 27096 Z= 0.419 Angle : 0.851 27.819 36832 Z= 0.475 Chirality : 0.055 0.823 4224 Planarity : 0.005 0.091 4856 Dihedral : 6.302 59.385 3616 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer Outliers : 4.53 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.74 % 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: -0.03 (0.14), residues: 3368 helix: 0.28 (0.24), residues: 568 sheet: 1.22 (0.15), residues: 966 loop : -0.81 (0.15), residues: 1834 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 251 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 89 residues processed: 345 average time/residue: 1.3109 time to fit residues: 532.7892 Evaluate side-chains 330 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 241 time to evaluate : 3.198 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 64 residues processed: 25 average time/residue: 0.5180 time to fit residues: 22.6363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 8.9990 chunk 129 optimal weight: 0.0020 chunk 193 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 30 optimal weight: 40.0000 chunk 254 optimal weight: 9.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 476 ASN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 ASN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 ASN F 277 GLN F 280 GLN ** F 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN ** G 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.240 27096 Z= 0.442 Angle : 0.843 27.236 36832 Z= 0.471 Chirality : 0.052 0.617 4224 Planarity : 0.005 0.088 4856 Dihedral : 6.351 58.016 3616 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer Outliers : 4.37 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.74 % 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: -0.07 (0.14), residues: 3368 helix: 0.28 (0.24), residues: 562 sheet: 1.18 (0.15), residues: 996 loop : -0.87 (0.15), residues: 1810 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 243 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 87 residues processed: 332 average time/residue: 1.3580 time to fit residues: 525.8218 Evaluate side-chains 315 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 228 time to evaluate : 3.937 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 63 residues processed: 24 average time/residue: 0.4489 time to fit residues: 20.2343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 301 optimal weight: 6.9990 chunk 181 optimal weight: 30.0000 chunk 131 optimal weight: 0.0050 chunk 236 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 272 optimal weight: 0.7980 chunk 285 optimal weight: 0.5980 chunk 300 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 476 ASN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 403 GLN F 424 GLN F 499 ASN ** G 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN ** H 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.239 27096 Z= 0.357 Angle : 0.816 27.397 36832 Z= 0.454 Chirality : 0.049 0.378 4224 Planarity : 0.005 0.085 4856 Dihedral : 5.910 50.769 3616 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: 0.38 (0.15), residues: 3368 helix: 0.73 (0.26), residues: 535 sheet: 1.31 (0.16), residues: 991 loop : -0.48 (0.15), residues: 1842 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 264 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 64 residues processed: 332 average time/residue: 1.3086 time to fit residues: 513.4959 Evaluate side-chains 304 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 240 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 52 residues processed: 12 average time/residue: 0.8158 time to fit residues: 16.8742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 3.9990 chunk 319 optimal weight: 0.1980 chunk 194 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 chunk 308 optimal weight: 8.9990 chunk 266 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 476 ASN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 499 ASN D 388 ASN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 GLN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN ** G 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN ** H 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.239 27096 Z= 0.377 Angle : 0.814 27.165 36832 Z= 0.453 Chirality : 0.050 0.382 4224 Planarity : 0.005 0.082 4856 Dihedral : 5.975 52.374 3616 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: 0.40 (0.15), residues: 3368 helix: 0.70 (0.26), residues: 529 sheet: 1.36 (0.16), residues: 1005 loop : -0.49 (0.15), residues: 1834 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 255 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 62 residues processed: 320 average time/residue: 1.3357 time to fit residues: 500.0167 Evaluate side-chains 310 residues out of total 3000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 248 time to evaluate : 3.293 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 53 residues processed: 9 average time/residue: 0.7168 time to fit residues: 12.8453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.9980 chunk 283 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 39 optimal weight: 50.0000 chunk 74 optimal weight: 0.6980 chunk 266 optimal weight: 0.3980 chunk 111 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 476 ASN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN D 388 ASN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 ASN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN ** G 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN ** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121104 restraints weight = 37080.607| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.16 r_work: 0.3268 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.238 27096 Z= 0.415 Angle : 0.843 27.298 36832 Z= 0.466 Chirality : 0.052 0.459 4224 Planarity : 0.005 0.082 4856 Dihedral : 6.129 52.093 3616 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.04 (0.15), residues: 3368 helix: 0.32 (0.24), residues: 564 sheet: 1.28 (0.16), residues: 983 loop : -0.79 (0.15), residues: 1821 =============================================================================== Job complete usr+sys time: 10104.49 seconds wall clock time: 181 minutes 0.15 seconds (10860.15 seconds total)