Starting phenix.real_space_refine (version: dev) on Wed Apr 6 21:51:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/04_2022/3j9c_6224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/04_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_6224/04_2022/3j9c_6224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/04_2022/3j9c_6224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/04_2022/3j9c_6224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9c_6224/04_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 "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E GLU 515": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G GLU 515": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 23296 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3328 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2, 'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 403, None: 2, 'PCIS': 1} Not linked: pdbres="PHE A 596 " pdbres=" CA A 801 " Not linked: pdbres=" CA A 801 " pdbres=" CA A 802 " Chain: "B" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3328 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2, 'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 403, None: 2, 'PCIS': 1} Not linked: pdbres="PHE B 596 " pdbres=" CA B 801 " Not linked: pdbres=" CA B 801 " pdbres=" CA B 802 " Chain: "C" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3328 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2, 'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 403, None: 2, 'PCIS': 1} 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: {'undetermined': 2, 'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 403, None: 2, 'PCIS': 1} 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: {'undetermined': 2, 'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 403, None: 2, 'PCIS': 1} 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: {'undetermined': 2, 'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 403, None: 2, 'PCIS': 1} 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: {'undetermined': 2, 'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 403, None: 2, 'PCIS': 1} Not linked: pdbres="PHE G 596 " pdbres=" CA G 801 " Not linked: pdbres=" CA G 801 " pdbres=" CA G 802 " Time building chain proxies: 13.70, per 1000 atoms: 0.59 Number of scatterers: 23296 At special positions: 0 Unit cell: (143.36, 140.8, 199.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 35 16.00 O 4697 8.00 N 4046 7.00 C 14504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.11 Conformation dependent library (CDL) restraints added in 3.9 seconds 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5656 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 63 sheets defined 20.8% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS A 518 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR A 576 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 578 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 476 through 486 removed outlier: 3.821A pdb=" N VAL B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.610A pdb=" N LYS B 518 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR B 576 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 578 " --> pdb=" O TYR B 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 476 through 486 removed outlier: 3.821A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS C 518 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 532 Processing helix chain 'C' and resid 555 through 569 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR C 576 " --> pdb=" O ASN C 573 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 578 " --> pdb=" O TYR C 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL D 480 " --> pdb=" O ASN D 476 " (cutoff:3.500A) Proline residue: D 482 - end of helix Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 532 Processing helix chain 'D' and resid 555 through 569 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR D 576 " --> pdb=" O ASN D 573 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU D 578 " --> pdb=" O TYR D 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Proline residue: E 482 - end of helix Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS E 518 " --> pdb=" O GLU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 Processing helix chain 'E' and resid 555 through 569 Processing helix chain 'E' and resid 573 through 578 removed outlier: 3.567A pdb=" N THR E 576 " --> pdb=" O ASN E 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU E 578 " --> pdb=" O TYR E 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.690A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.775A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL F 480 " --> pdb=" O ASN F 476 " (cutoff:3.500A) Proline residue: F 482 - end of helix Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS F 518 " --> pdb=" O GLU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 532 Processing helix chain 'F' and resid 555 through 569 Processing helix chain 'F' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR F 576 " --> pdb=" O ASN F 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU F 578 " --> pdb=" O TYR F 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 212 removed outlier: 3.689A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.774A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 476 through 486 removed outlier: 3.822A pdb=" N VAL G 480 " --> pdb=" O ASN G 476 " (cutoff:3.500A) Proline residue: G 482 - end of helix Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.609A pdb=" N LYS G 518 " --> pdb=" O GLU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 Processing helix chain 'G' and resid 555 through 569 Processing helix chain 'G' and resid 573 through 578 removed outlier: 3.568A pdb=" N THR G 576 " --> pdb=" O ASN G 573 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU G 578 " --> pdb=" O TYR G 575 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 192 through 196 Processing sheet with id= 2, first strand: chain 'A' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL A 264 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 367 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET A 266 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG A 365 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 268 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 432 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 276 through 299 Processing sheet with id= 5, first strand: chain 'A' and resid 302 through 311 Processing sheet with id= 6, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN A 376 " --> pdb=" O ASN A 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN A 458 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 454 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER A 382 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR A 452 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 384 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A 450 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 460 through 462 Processing sheet with id= 8, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 541 through 542 Processing sheet with id= 10, first strand: chain 'B' and resid 192 through 196 Processing sheet with id= 11, first strand: chain 'B' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL B 264 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 367 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET B 266 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG B 365 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 268 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 276 through 299 Processing sheet with id= 14, first strand: chain 'B' and resid 302 through 311 Processing sheet with id= 15, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN B 376 " --> pdb=" O ASN B 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN B 458 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 454 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER B 382 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR B 452 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 384 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 450 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 460 through 462 Processing sheet with id= 17, first strand: chain 'B' and resid 501 through 506 removed outlier: 8.445A pdb=" N ILE B 589 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 541 through 542 Processing sheet with id= 19, first strand: chain 'C' and resid 192 through 196 Processing sheet with id= 20, first strand: chain 'C' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL C 264 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 367 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N MET C 266 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG C 365 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 268 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 409 through 411 removed outlier: 3.799A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 432 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 276 through 299 Processing sheet with id= 23, first strand: chain 'C' and resid 302 through 311 Processing sheet with id= 24, first strand: chain 'C' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN C 376 " --> pdb=" O ASN C 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN C 458 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN C 454 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER C 382 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR C 452 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C 384 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU C 450 " --> pdb=" O VAL C 384 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 460 through 462 Processing sheet with id= 26, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 541 through 542 Processing sheet with id= 28, first strand: chain 'D' and resid 192 through 196 Processing sheet with id= 29, first strand: chain 'D' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL D 264 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL D 367 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET D 266 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG D 365 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D 268 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.799A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE D 432 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 276 through 299 Processing sheet with id= 32, first strand: chain 'D' and resid 302 through 311 Processing sheet with id= 33, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN D 376 " --> pdb=" O ASN D 458 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASN D 458 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 454 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER D 382 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR D 452 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL D 384 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D 450 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 460 through 462 Processing sheet with id= 35, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 541 through 542 Processing sheet with id= 37, first strand: chain 'E' and resid 192 through 196 Processing sheet with id= 38, first strand: chain 'E' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL E 264 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL E 367 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET E 266 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG E 365 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 268 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'E' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE E 432 " --> pdb=" O LEU E 360 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'E' and resid 276 through 299 Processing sheet with id= 41, first strand: chain 'E' and resid 302 through 311 Processing sheet with id= 42, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN E 376 " --> pdb=" O ASN E 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN E 458 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN E 454 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER E 382 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR E 452 " --> pdb=" O SER E 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL E 384 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU E 450 " --> pdb=" O VAL E 384 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'E' and resid 460 through 462 Processing sheet with id= 44, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 541 through 542 Processing sheet with id= 46, first strand: chain 'F' and resid 192 through 196 Processing sheet with id= 47, first strand: chain 'F' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL F 264 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL F 367 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET F 266 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG F 365 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 268 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'F' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE F 432 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'F' and resid 276 through 299 Processing sheet with id= 50, first strand: chain 'F' and resid 302 through 311 Processing sheet with id= 51, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.681A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN F 376 " --> pdb=" O ASN F 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN F 458 " --> pdb=" O ASN F 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN F 454 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER F 382 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR F 452 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL F 384 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU F 450 " --> pdb=" O VAL F 384 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'F' and resid 460 through 462 Processing sheet with id= 53, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.444A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'F' and resid 541 through 542 Processing sheet with id= 55, first strand: chain 'G' and resid 192 through 196 Processing sheet with id= 56, first strand: chain 'G' and resid 262 through 273 removed outlier: 5.730A pdb=" N VAL G 264 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL G 367 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N MET G 266 " --> pdb=" O ARG G 365 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG G 365 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN G 268 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'G' and resid 409 through 411 removed outlier: 3.800A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE G 432 " --> pdb=" O LEU G 360 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'G' and resid 276 through 299 Processing sheet with id= 59, first strand: chain 'G' and resid 302 through 311 Processing sheet with id= 60, first strand: chain 'G' and resid 389 through 395 removed outlier: 6.682A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASN G 376 " --> pdb=" O ASN G 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASN G 458 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN G 454 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER G 382 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR G 452 " --> pdb=" O SER G 382 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL G 384 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU G 450 " --> pdb=" O VAL G 384 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'G' and resid 460 through 462 Processing sheet with id= 62, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.445A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'G' and resid 541 through 542 805 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.98 Time building geometry restraints manager: 10.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7766 1.34 - 1.45: 2865 1.45 - 1.57: 13001 1.57 - 1.69: 7 1.69 - 1.81: 70 Bond restraints: 23709 Sorted by residual: bond pdb=" CA LYS F 444 " pdb=" C LYS F 444 " ideal model delta sigma weight residual 1.523 1.606 -0.082 1.34e-02 5.57e+03 3.78e+01 bond pdb=" CA LYS D 444 " pdb=" C LYS D 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.75e+01 bond pdb=" CA LYS E 444 " pdb=" C LYS E 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.73e+01 bond pdb=" CA LYS G 444 " pdb=" C LYS G 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.73e+01 bond pdb=" CA LYS A 444 " pdb=" C LYS A 444 " ideal model delta sigma weight residual 1.523 1.605 -0.082 1.34e-02 5.57e+03 3.72e+01 ... (remaining 23704 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.16: 618 106.16 - 113.12: 12895 113.12 - 120.07: 7509 120.07 - 127.03: 11064 127.03 - 133.98: 142 Bond angle restraints: 32228 Sorted by residual: angle pdb=" C ALA G 417 " pdb=" N PRO G 418 " pdb=" CA PRO G 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.97e+01 angle pdb=" C ALA B 417 " pdb=" N PRO B 418 " pdb=" CA PRO B 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.97e+01 angle pdb=" C ALA C 417 " pdb=" N PRO C 418 " pdb=" CA PRO C 418 " ideal model delta sigma weight residual 119.78 125.39 -5.61 1.03e+00 9.43e-01 2.96e+01 angle pdb=" C ALA A 417 " pdb=" N PRO A 418 " pdb=" CA PRO A 418 " ideal model delta sigma weight residual 119.78 125.37 -5.59 1.03e+00 9.43e-01 2.95e+01 angle pdb=" C ALA E 417 " pdb=" N PRO E 418 " pdb=" CA PRO E 418 " ideal model delta sigma weight residual 119.78 125.37 -5.59 1.03e+00 9.43e-01 2.94e+01 ... (remaining 32223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.73: 12750 13.73 - 27.45: 1068 27.45 - 41.17: 378 41.17 - 54.90: 189 54.90 - 68.62: 84 Dihedral angle restraints: 14469 sinusoidal: 5768 harmonic: 8701 Sorted by residual: dihedral pdb=" CA SER D 413 " pdb=" C SER D 413 " pdb=" N LYS D 414 " pdb=" CA LYS D 414 " ideal model delta harmonic sigma weight residual 180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER G 413 " pdb=" C SER G 413 " pdb=" N LYS G 414 " pdb=" CA LYS G 414 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER B 413 " pdb=" C SER B 413 " pdb=" N LYS B 414 " pdb=" CA LYS B 414 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 14466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2892 0.050 - 0.100: 611 0.100 - 0.150: 172 0.150 - 0.200: 7 0.200 - 0.249: 14 Chirality restraints: 3696 Sorted by residual: chirality pdb=" CA LYS E 444 " pdb=" N LYS E 444 " pdb=" C LYS E 444 " pdb=" CB LYS E 444 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA LYS D 444 " pdb=" N LYS D 444 " pdb=" C LYS D 444 " pdb=" CB LYS D 444 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA GLN D 543 " pdb=" N GLN D 543 " pdb=" C GLN D 543 " pdb=" CB GLN D 543 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3693 not shown) Planarity restraints: 4249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 378 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO E 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 379 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 378 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO B 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 379 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 378 " 0.028 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO F 379 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO F 379 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 379 " 0.024 5.00e-02 4.00e+02 ... (remaining 4246 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6068 2.80 - 3.33: 21651 3.33 - 3.85: 40621 3.85 - 4.38: 48843 4.38 - 4.90: 82492 Nonbonded interactions: 199675 Sorted by model distance: nonbonded pdb=" O ILE C 183 " pdb="CA CA C 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE F 183 " pdb="CA CA F 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE E 183 " pdb="CA CA E 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE D 183 " pdb="CA CA D 801 " model vdw 2.277 2.510 nonbonded pdb=" O ILE A 183 " pdb="CA CA A 801 " model vdw 2.277 2.510 ... (remaining 199670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 35 5.16 5 C 14504 2.51 5 N 4046 2.21 5 O 4697 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.550 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.200 Process input model: 63.010 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 23709 Z= 0.353 Angle : 1.112 10.831 32228 Z= 0.743 Chirality : 0.047 0.249 3696 Planarity : 0.004 0.043 4249 Dihedral : 14.410 68.624 8813 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 6.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2947 helix: -1.67 (0.20), residues: 497 sheet: -0.98 (0.15), residues: 1001 loop : 0.51 (0.18), residues: 1449 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 600 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 17 residues processed: 706 average time/residue: 1.2817 time to fit residues: 1037.3474 Evaluate side-chains 338 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 321 time to evaluate : 2.816 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 3.8217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 123 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 140 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 424 GLN A 483 GLN A 499 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN B 274 ASN B 483 GLN B 557 GLN C 389 GLN C 483 GLN C 537 ASN C 541 GLN D 198 ASN D 274 ASN D 424 GLN D 499 ASN ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS E 274 ASN E 285 GLN E 389 GLN E 424 GLN E 483 GLN E 557 GLN E 570 ASN F 209 ASN F 274 ASN F 389 GLN F 483 GLN F 499 ASN G 198 ASN G 209 ASN G 274 ASN G 285 GLN G 424 GLN G 483 GLN G 560 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 23709 Z= 0.345 Angle : 0.610 5.603 32228 Z= 0.328 Chirality : 0.049 0.164 3696 Planarity : 0.005 0.077 4249 Dihedral : 5.535 20.692 3164 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 5.22 % 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: -0.22 (0.15), residues: 2947 helix: -0.25 (0.24), residues: 504 sheet: 0.32 (0.16), residues: 875 loop : -0.29 (0.16), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 318 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 65 residues processed: 407 average time/residue: 1.4157 time to fit residues: 655.7364 Evaluate side-chains 338 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 273 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 43 residues processed: 22 average time/residue: 0.3207 time to fit residues: 14.9736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 222 optimal weight: 30.0000 chunk 181 optimal weight: 40.0000 chunk 73 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 265 optimal weight: 40.0000 chunk 91 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 424 GLN A 476 ASN A 537 ASN A 541 GLN B 424 GLN B 476 ASN B 557 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 ASN D 541 GLN E 285 GLN E 424 GLN E 476 ASN E 560 GLN F 285 GLN F 389 GLN F 476 ASN G 285 GLN ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN G 541 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 23709 Z= 0.231 Angle : 0.521 6.318 32228 Z= 0.279 Chirality : 0.046 0.162 3696 Planarity : 0.004 0.054 4249 Dihedral : 5.028 19.976 3164 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 4.34 % 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: -0.03 (0.15), residues: 2947 helix: 0.08 (0.25), residues: 504 sheet: 0.82 (0.17), residues: 875 loop : -0.50 (0.16), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 272 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 70 residues processed: 354 average time/residue: 1.3638 time to fit residues: 551.2041 Evaluate side-chains 323 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 253 time to evaluate : 2.840 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 49 residues processed: 21 average time/residue: 0.3690 time to fit residues: 15.7539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 138 optimal weight: 30.0000 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 254 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 285 GLN B 424 GLN B 476 ASN C 476 ASN D 476 ASN E 285 GLN E 422 ASN E 424 GLN E 476 ASN F 198 ASN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 476 ASN F 560 GLN G 424 GLN ** G 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 23709 Z= 0.351 Angle : 0.561 6.115 32228 Z= 0.298 Chirality : 0.048 0.160 3696 Planarity : 0.005 0.047 4249 Dihedral : 5.202 19.576 3164 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 5.79 % 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: -0.13 (0.15), residues: 2947 helix: 0.02 (0.25), residues: 497 sheet: 0.96 (0.16), residues: 875 loop : -0.72 (0.15), residues: 1575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 251 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 91 residues processed: 354 average time/residue: 1.4159 time to fit residues: 573.0240 Evaluate side-chains 331 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 240 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 61 residues processed: 30 average time/residue: 0.4361 time to fit residues: 22.7611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 0.3980 chunk 255 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN A 541 GLN B 285 GLN B 424 GLN B 476 ASN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN E 403 GLN E 424 GLN E 476 ASN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN G 537 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 23709 Z= 0.183 Angle : 0.491 7.145 32228 Z= 0.261 Chirality : 0.045 0.158 3696 Planarity : 0.004 0.041 4249 Dihedral : 4.777 18.763 3164 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 4.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2947 helix: 0.23 (0.25), residues: 504 sheet: 1.18 (0.16), residues: 903 loop : -0.60 (0.16), residues: 1540 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 254 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 71 residues processed: 336 average time/residue: 1.3422 time to fit residues: 517.2120 Evaluate side-chains 320 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 249 time to evaluate : 2.840 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 54 residues processed: 17 average time/residue: 0.5524 time to fit residues: 16.2618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 166 optimal weight: 0.0270 chunk 70 optimal weight: 0.8980 chunk 284 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 94 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 424 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 403 GLN B 424 GLN ** B 476 ASN ** 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 285 GLN E 422 ASN F 422 ASN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 23709 Z= 0.134 Angle : 0.474 9.340 32228 Z= 0.249 Chirality : 0.044 0.154 3696 Planarity : 0.004 0.038 4249 Dihedral : 4.466 18.663 3164 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 3.50 % 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: 0.62 (0.16), residues: 2947 helix: 0.77 (0.28), residues: 462 sheet: 1.43 (0.16), residues: 903 loop : -0.27 (0.16), residues: 1582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 276 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 65 residues processed: 337 average time/residue: 1.3620 time to fit residues: 535.0273 Evaluate side-chains 313 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 248 time to evaluate : 2.572 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 48 residues processed: 18 average time/residue: 0.5235 time to fit residues: 17.1601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 0.0770 chunk 32 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 239 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 130 optimal weight: 0.1980 overall best weight: 3.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 422 ASN B 424 GLN B 476 ASN C 476 ASN D 476 ASN E 285 GLN E 422 ASN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 560 GLN ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 23709 Z= 0.297 Angle : 0.544 9.744 32228 Z= 0.286 Chirality : 0.046 0.157 3696 Planarity : 0.004 0.039 4249 Dihedral : 4.837 19.038 3164 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 4.53 % 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: 0.48 (0.15), residues: 2947 helix: 0.67 (0.27), residues: 448 sheet: 1.40 (0.16), residues: 903 loop : -0.41 (0.16), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 249 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 85 residues processed: 320 average time/residue: 1.3458 time to fit residues: 495.2643 Evaluate side-chains 325 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 240 time to evaluate : 2.907 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 54 residues processed: 31 average time/residue: 0.3827 time to fit residues: 21.4631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 169 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 0.0570 chunk 54 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 193 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 222 optimal weight: 30.0000 overall best weight: 2.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 424 GLN B 476 ASN C 476 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN E 499 ASN F 422 ASN ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 23709 Z= 0.238 Angle : 0.524 9.151 32228 Z= 0.275 Chirality : 0.045 0.161 3696 Planarity : 0.004 0.036 4249 Dihedral : 4.716 18.945 3164 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 4.00 % 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: 0.44 (0.15), residues: 2947 helix: 0.64 (0.27), residues: 455 sheet: 1.41 (0.16), residues: 903 loop : -0.47 (0.16), residues: 1589 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 239 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 78 residues processed: 309 average time/residue: 1.3544 time to fit residues: 480.3096 Evaluate side-chains 313 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 235 time to evaluate : 2.836 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 56 residues processed: 23 average time/residue: 0.3706 time to fit residues: 16.5242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 chunk 264 optimal weight: 30.0000 chunk 158 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 403 GLN B 424 GLN B 476 ASN C 476 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 560 GLN ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 23709 Z= 0.351 Angle : 0.574 11.697 32228 Z= 0.299 Chirality : 0.048 0.160 3696 Planarity : 0.005 0.040 4249 Dihedral : 4.989 19.163 3164 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 4.08 % 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: 0.07 (0.15), residues: 2947 helix: 0.20 (0.25), residues: 490 sheet: 1.11 (0.15), residues: 959 loop : -0.71 (0.16), residues: 1498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 238 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 81 residues processed: 309 average time/residue: 1.3622 time to fit residues: 485.3613 Evaluate side-chains 312 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 231 time to evaluate : 2.846 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 61 residues processed: 20 average time/residue: 0.4017 time to fit residues: 15.8606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 292 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 180 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 424 GLN B 476 ASN C 476 ASN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** F 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 23709 Z= 0.376 Angle : 0.589 12.870 32228 Z= 0.307 Chirality : 0.048 0.162 3696 Planarity : 0.005 0.040 4249 Dihedral : 5.051 18.909 3164 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 3.73 % 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: -0.08 (0.15), residues: 2947 helix: 0.08 (0.25), residues: 490 sheet: 0.99 (0.15), residues: 959 loop : -0.78 (0.16), residues: 1498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 235 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 78 residues processed: 302 average time/residue: 1.3921 time to fit residues: 482.7978 Evaluate side-chains 307 residues out of total 2625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 229 time to evaluate : 2.902 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 60 residues processed: 18 average time/residue: 0.5156 time to fit residues: 16.8106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 215 optimal weight: 0.0050 chunk 34 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 476 ASN B 424 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN ** G 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103276 restraints weight = 32487.822| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.79 r_work: 0.3208 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 1.60 restraints_weight: 0.2500 r_work: 0.3177 rms_B_bonded: 1.69 restraints_weight: 0.1250 r_work: 0.3159 rms_B_bonded: 1.86 restraints_weight: 0.0625 r_work: 0.3137 rms_B_bonded: 2.11 restraints_weight: 0.0312 r_work: 0.3112 rms_B_bonded: 2.45 restraints_weight: 0.0156 r_work: 0.3081 rms_B_bonded: 2.90 restraints_weight: 0.0078 r_work: 0.3045 rms_B_bonded: 3.50 restraints_weight: 0.0039 r_work: 0.2999 rms_B_bonded: 4.30 restraints_weight: 0.0020 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 23709 Z= 0.158 Angle : 0.507 10.455 32228 Z= 0.265 Chirality : 0.044 0.157 3696 Planarity : 0.004 0.034 4249 Dihedral : 4.611 18.908 3164 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 2.97 % 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: 0.29 (0.15), residues: 2947 helix: 0.43 (0.26), residues: 497 sheet: 1.42 (0.16), residues: 903 loop : -0.63 (0.15), residues: 1547 =============================================================================== Job complete usr+sys time: 8172.03 seconds wall clock time: 146 minutes 44.60 seconds (8804.60 seconds total)