Starting phenix.real_space_refine on Mon Jul 22 10:30:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/07_2024/7n5e_24187.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/07_2024/7n5e_24187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/07_2024/7n5e_24187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/07_2024/7n5e_24187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/07_2024/7n5e_24187.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5e_24187/07_2024/7n5e_24187.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 11784 2.51 5 N 2960 2.21 5 O 3094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 625": "OE1" <-> "OE2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 746": "OE1" <-> "OE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 611": "OE1" <-> "OE2" Residue "G PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 695": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17915 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2579 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 7, 'TRANS': 308} Chain breaks: 2 Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "E" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "F" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.70, per 1000 atoms: 0.54 Number of scatterers: 17915 At special positions: 0 Unit cell: (147.29, 144.2, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 3094 8.00 N 2960 7.00 C 11784 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: 6.93 Conformation dependent library (CDL) restraints added in 3.3 seconds 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 9 sheets defined 59.3% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 295 through 333 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 504 through 552 Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 661 through 678 Processing helix chain 'A' and resid 714 through 737 Processing helix chain 'B' and resid 295 through 329 removed outlier: 3.824A pdb=" N LEU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 331 No H-bonds generated for 'chain 'B' and resid 330 through 331' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 590 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 661 through 678 Processing helix chain 'B' and resid 714 through 737 Processing helix chain 'C' and resid 295 through 329 removed outlier: 3.892A pdb=" N SER C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 331 No H-bonds generated for 'chain 'C' and resid 330 through 331' Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.519A pdb=" N GLN C 350 " --> pdb=" O HIS C 346 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 524 Processing helix chain 'C' and resid 526 through 552 Processing helix chain 'C' and resid 556 through 590 removed outlier: 5.551A pdb=" N ASN C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'C' and resid 661 through 678 Processing helix chain 'C' and resid 714 through 737 Processing helix chain 'D' and resid 295 through 327 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 352 removed outlier: 3.541A pdb=" N GLN D 350 " --> pdb=" O HIS D 346 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR D 351 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 524 Processing helix chain 'D' and resid 526 through 552 Processing helix chain 'D' and resid 556 through 590 removed outlier: 5.586A pdb=" N ASN D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 635 Processing helix chain 'D' and resid 661 through 678 Processing helix chain 'D' and resid 714 through 737 Processing helix chain 'E' and resid 295 through 327 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 352 removed outlier: 3.661A pdb=" N GLN E 350 " --> pdb=" O HIS E 346 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR E 351 " --> pdb=" O SER E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 524 Processing helix chain 'E' and resid 526 through 552 Processing helix chain 'E' and resid 556 through 590 removed outlier: 5.669A pdb=" N ASN E 576 " --> pdb=" O PHE E 572 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR E 577 " --> pdb=" O ILE E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 635 Processing helix chain 'E' and resid 661 through 678 Processing helix chain 'E' and resid 714 through 736 Processing helix chain 'F' and resid 295 through 329 removed outlier: 3.985A pdb=" N SER F 329 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 331 No H-bonds generated for 'chain 'F' and resid 330 through 331' Processing helix chain 'F' and resid 332 through 334 No H-bonds generated for 'chain 'F' and resid 332 through 334' Processing helix chain 'F' and resid 335 through 352 Processing helix chain 'F' and resid 508 through 524 Processing helix chain 'F' and resid 526 through 552 Processing helix chain 'F' and resid 556 through 590 removed outlier: 5.688A pdb=" N ASN F 576 " --> pdb=" O PHE F 572 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 661 through 678 Processing helix chain 'F' and resid 714 through 737 Processing helix chain 'G' and resid 295 through 329 removed outlier: 3.906A pdb=" N SER G 329 " --> pdb=" O ILE G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 331 No H-bonds generated for 'chain 'G' and resid 330 through 331' Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 352 Processing helix chain 'G' and resid 508 through 524 Processing helix chain 'G' and resid 526 through 552 Processing helix chain 'G' and resid 556 through 590 removed outlier: 5.688A pdb=" N ASN G 576 " --> pdb=" O PHE G 572 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 635 Processing helix chain 'G' and resid 661 through 678 Processing helix chain 'G' and resid 714 through 737 Processing sheet with id=AA1, first strand: chain 'A' and resid 599 through 602 removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 626 " --> pdb=" O ASN B 641 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 626 " --> pdb=" O ASN C 641 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 618 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N MET C 612 " --> pdb=" O THR C 616 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR C 616 " --> pdb=" O MET C 612 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 626 " --> pdb=" O ASN D 641 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 618 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N MET D 612 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR D 616 " --> pdb=" O MET D 612 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS D 626 " --> pdb=" O ASN E 641 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL E 618 " --> pdb=" O GLU E 610 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET E 612 " --> pdb=" O THR E 616 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR E 616 " --> pdb=" O MET E 612 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS E 626 " --> pdb=" O ASN F 641 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL F 618 " --> pdb=" O GLU F 610 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS F 626 " --> pdb=" O ASN G 641 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL G 618 " --> pdb=" O GLU G 610 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N MET G 612 " --> pdb=" O THR G 616 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR G 616 " --> pdb=" O MET G 612 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS G 626 " --> pdb=" O ASN A 641 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.531A pdb=" N LYS A 699 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 694 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS A 701 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 707 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 686 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 745 through 750 removed outlier: 6.485A pdb=" N GLN A 745 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG B 750 " --> pdb=" O GLN A 745 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE A 747 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE G 749 " --> pdb=" O ARG A 750 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.484A pdb=" N LYS B 699 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 694 " --> pdb=" O LYS B 699 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 701 " --> pdb=" O LYS B 692 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 649 through 657 removed outlier: 6.416A pdb=" N LYS C 699 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE C 694 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS C 701 " --> pdb=" O LYS C 692 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 707 " --> pdb=" O GLN C 686 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN C 686 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 649 through 657 removed outlier: 6.507A pdb=" N LYS D 699 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE D 694 " --> pdb=" O LYS D 699 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS D 701 " --> pdb=" O LYS D 692 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 649 through 657 removed outlier: 6.465A pdb=" N LYS E 699 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE E 694 " --> pdb=" O LYS E 699 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS E 701 " --> pdb=" O LYS E 692 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 649 through 657 removed outlier: 6.506A pdb=" N LYS F 699 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE F 694 " --> pdb=" O LYS F 699 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS F 701 " --> pdb=" O LYS F 692 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN F 707 " --> pdb=" O GLN F 686 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN F 686 " --> pdb=" O ASN F 707 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 649 through 657 removed outlier: 6.330A pdb=" N LYS G 699 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE G 694 " --> pdb=" O LYS G 699 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS G 701 " --> pdb=" O LYS G 692 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN G 707 " --> pdb=" O GLN G 686 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN G 686 " --> pdb=" O ASN G 707 " (cutoff:3.500A) 1231 hydrogen bonds defined for protein. 3618 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: 5.31 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3350 1.31 - 1.44: 4632 1.44 - 1.56: 10105 1.56 - 1.69: 59 1.69 - 1.81: 133 Bond restraints: 18279 Sorted by residual: bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.47e+01 bond pdb=" CD2 TRP D 507 " pdb=" CE3 TRP D 507 " ideal model delta sigma weight residual 1.398 1.505 -0.107 1.60e-02 3.91e+03 4.46e+01 bond pdb=" CD2 TRP B 507 " pdb=" CE3 TRP B 507 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.28e+01 bond pdb=" CZ2 TRP C 507 " pdb=" CH2 TRP C 507 " ideal model delta sigma weight residual 1.368 1.486 -0.118 1.90e-02 2.77e+03 3.82e+01 bond pdb=" CZ2 TRP E 507 " pdb=" CH2 TRP E 507 " ideal model delta sigma weight residual 1.368 1.483 -0.115 1.90e-02 2.77e+03 3.64e+01 ... (remaining 18274 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.71: 327 105.71 - 112.90: 9671 112.90 - 120.09: 7770 120.09 - 127.27: 6750 127.27 - 134.46: 198 Bond angle restraints: 24716 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.08 -8.28 1.00e+00 1.00e+00 6.86e+01 angle pdb=" C GLN G 291 " pdb=" N PRO G 292 " pdb=" CA PRO G 292 " ideal model delta sigma weight residual 119.47 128.27 -8.80 1.16e+00 7.43e-01 5.76e+01 angle pdb=" C GLN C 291 " pdb=" N PRO C 292 " pdb=" CA PRO C 292 " ideal model delta sigma weight residual 119.56 127.00 -7.44 1.02e+00 9.61e-01 5.32e+01 angle pdb=" N THR C 557 " pdb=" CA THR C 557 " pdb=" C THR C 557 " ideal model delta sigma weight residual 112.89 121.73 -8.84 1.24e+00 6.50e-01 5.08e+01 angle pdb=" C HIS E 592 " pdb=" N PRO E 593 " pdb=" CA PRO E 593 " ideal model delta sigma weight residual 119.56 126.71 -7.15 1.01e+00 9.80e-01 5.02e+01 ... (remaining 24711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10586 17.71 - 35.42: 253 35.42 - 53.13: 50 53.13 - 70.84: 30 70.84 - 88.54: 12 Dihedral angle restraints: 10931 sinusoidal: 4511 harmonic: 6420 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.54 88.54 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 10928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2091 0.092 - 0.185: 712 0.185 - 0.277: 110 0.277 - 0.370: 17 0.370 - 0.462: 1 Chirality restraints: 2931 Sorted by residual: chirality pdb=" CA THR C 557 " pdb=" N THR C 557 " pdb=" C THR C 557 " pdb=" CB THR C 557 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA TRP B 304 " pdb=" N TRP B 304 " pdb=" C TRP B 304 " pdb=" CB TRP B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA THR G 557 " pdb=" N THR G 557 " pdb=" C THR G 557 " pdb=" CB THR G 557 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 2928 not shown) Planarity restraints: 3023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 291 " 0.022 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLN E 291 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN E 291 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO E 292 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 675 " 0.044 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR E 675 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR E 675 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 675 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 675 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 675 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR E 675 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 675 " 0.042 2.00e-02 2.50e+03 ... (remaining 3020 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 6714 2.88 - 3.39: 18129 3.39 - 3.89: 30327 3.89 - 4.40: 34802 4.40 - 4.90: 56059 Nonbonded interactions: 146031 Sorted by model distance: nonbonded pdb=" OD1 ASP F 737 " pdb=" NZ LYS F 739 " model vdw 2.378 2.520 nonbonded pdb=" OD1 ASP G 737 " pdb=" NZ LYS G 739 " model vdw 2.385 2.520 nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 2.520 nonbonded pdb=" OD1 ASP D 737 " pdb=" NZ LYS D 739 " model vdw 2.399 2.520 nonbonded pdb=" OD1 ASP E 737 " pdb=" NZ LYS E 739 " model vdw 2.399 2.520 ... (remaining 146026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 294 through 354 or resid 507 through 751 or resid 801)) selection = (chain 'B' and (resid 294 through 751 or resid 801)) selection = (chain 'C' and (resid 294 through 751 or resid 801)) selection = (chain 'D' and (resid 294 through 751 or resid 801)) selection = (chain 'E' and (resid 294 through 751 or resid 801)) selection = (chain 'F' and (resid 294 through 751 or resid 801)) selection = (chain 'G' and (resid 294 through 751 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 47.240 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.023 0.132 18279 Z= 1.473 Angle : 1.544 8.842 24716 Z= 1.056 Chirality : 0.090 0.462 2931 Planarity : 0.008 0.043 3023 Dihedral : 10.255 88.544 6707 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.17), residues: 2146 helix: 1.62 (0.13), residues: 1206 sheet: 0.56 (0.31), residues: 290 loop : 1.09 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.010 TRP E 683 HIS 0.010 0.002 HIS A 331 PHE 0.059 0.006 PHE A 335 TYR 0.044 0.009 TYR E 675 ARG 0.006 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 2.031 Fit side-chains revert: symmetry clash REVERT: A 541 ILE cc_start: 0.8735 (mt) cc_final: 0.8435 (mt) REVERT: B 563 LEU cc_start: 0.8000 (tp) cc_final: 0.7773 (mm) REVERT: B 624 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7783 (mmtm) REVERT: C 526 LYS cc_start: 0.6893 (mttt) cc_final: 0.5990 (tptp) REVERT: C 595 ASP cc_start: 0.7265 (m-30) cc_final: 0.7001 (m-30) REVERT: D 701 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8330 (mmtp) REVERT: E 632 SER cc_start: 0.8136 (p) cc_final: 0.7909 (p) REVERT: E 717 GLU cc_start: 0.7571 (tp30) cc_final: 0.7356 (tp30) REVERT: E 737 ASP cc_start: 0.7125 (t0) cc_final: 0.6892 (t0) REVERT: G 324 LYS cc_start: 0.8490 (mttm) cc_final: 0.8271 (mttm) REVERT: G 525 ASN cc_start: 0.6814 (m-40) cc_final: 0.6601 (t0) REVERT: G 581 ILE cc_start: 0.8434 (mt) cc_final: 0.8105 (mt) REVERT: G 748 SER cc_start: 0.8818 (t) cc_final: 0.8614 (p) outliers start: 0 outliers final: 1 residues processed: 585 average time/residue: 1.3169 time to fit residues: 853.6670 Evaluate side-chains 508 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 507 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 547 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN C 345 HIS C 531 GLN C 648 GLN C 688 ASN C 698 ASN D 533 ASN D 713 GLN E 531 GLN E 648 GLN E 698 ASN F 345 HIS ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 576 ASN G 719 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18279 Z= 0.232 Angle : 0.557 6.801 24716 Z= 0.303 Chirality : 0.044 0.182 2931 Planarity : 0.004 0.044 3023 Dihedral : 7.446 58.971 2367 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.59 % Allowed : 9.83 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.15 (0.18), residues: 2146 helix: 3.06 (0.14), residues: 1202 sheet: 0.41 (0.27), residues: 329 loop : 1.16 (0.29), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 304 HIS 0.007 0.001 HIS A 331 PHE 0.022 0.002 PHE A 335 TYR 0.010 0.002 TYR D 740 ARG 0.005 0.000 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 526 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7704 (tttm) cc_final: 0.7400 (tttm) REVERT: B 624 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7909 (mmtm) REVERT: B 669 LYS cc_start: 0.8421 (mtpm) cc_final: 0.8141 (ttmm) REVERT: B 748 SER cc_start: 0.8364 (t) cc_final: 0.8115 (p) REVERT: C 526 LYS cc_start: 0.6631 (mttt) cc_final: 0.6058 (ttpp) REVERT: C 544 MET cc_start: 0.5018 (OUTLIER) cc_final: 0.4727 (mmp) REVERT: C 669 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7935 (mttm) REVERT: D 531 GLN cc_start: 0.7024 (mt0) cc_final: 0.6816 (mt0) REVERT: D 621 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7828 (mtmt) REVERT: D 644 ARG cc_start: 0.8493 (mtt180) cc_final: 0.8165 (mtt180) REVERT: D 650 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7936 (t0) REVERT: D 701 LYS cc_start: 0.8356 (mmtp) cc_final: 0.8120 (mmtp) REVERT: F 717 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8010 (mm-30) REVERT: G 324 LYS cc_start: 0.8470 (mttm) cc_final: 0.8250 (mttm) REVERT: G 545 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8030 (mm) REVERT: G 581 ILE cc_start: 0.8465 (mt) cc_final: 0.8094 (mt) REVERT: G 717 GLU cc_start: 0.7790 (tp30) cc_final: 0.7579 (tm-30) outliers start: 52 outliers final: 22 residues processed: 538 average time/residue: 1.2571 time to fit residues: 754.7991 Evaluate side-chains 532 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 507 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 568 VAL Chi-restraints excluded: chain G residue 580 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 chunk 67 optimal weight: 30.0000 chunk 158 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS A 686 GLN B 698 ASN C 531 GLN D 698 ASN E 531 GLN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 ASN G 531 GLN G 681 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18279 Z= 0.279 Angle : 0.522 9.252 24716 Z= 0.280 Chirality : 0.043 0.214 2931 Planarity : 0.003 0.045 3023 Dihedral : 7.433 59.699 2367 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.09 % Allowed : 11.72 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.20 (0.19), residues: 2146 helix: 3.25 (0.14), residues: 1202 sheet: 0.50 (0.27), residues: 329 loop : 0.79 (0.29), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 304 HIS 0.007 0.001 HIS F 684 PHE 0.022 0.002 PHE G 301 TYR 0.017 0.002 TYR E 740 ARG 0.006 0.000 ARG E 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 512 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7734 (tttm) cc_final: 0.7521 (tttm) REVERT: B 624 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7970 (mmtm) REVERT: B 669 LYS cc_start: 0.8427 (mtpm) cc_final: 0.8184 (ttmm) REVERT: B 673 LYS cc_start: 0.8728 (tttm) cc_final: 0.8510 (tttm) REVERT: B 701 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7978 (mtmm) REVERT: C 544 MET cc_start: 0.5252 (OUTLIER) cc_final: 0.4911 (mmp) REVERT: C 669 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7936 (mttm) REVERT: D 531 GLN cc_start: 0.7029 (mt0) cc_final: 0.6798 (mt0) REVERT: D 650 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7901 (t0) REVERT: D 710 ILE cc_start: 0.7844 (pt) cc_final: 0.7633 (pt) REVERT: E 737 ASP cc_start: 0.7018 (t0) cc_final: 0.6625 (t0) REVERT: F 671 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.8132 (mmm160) REVERT: G 324 LYS cc_start: 0.8528 (mttm) cc_final: 0.8310 (mttm) REVERT: G 689 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7989 (ttp) outliers start: 62 outliers final: 30 residues processed: 524 average time/residue: 1.3029 time to fit residues: 759.2927 Evaluate side-chains 532 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 498 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 635 CYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 539 ILE Chi-restraints excluded: chain G residue 568 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 689 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 198 optimal weight: 0.6980 chunk 209 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN E 531 GLN E 576 ASN E 648 GLN F 681 ASN ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 GLN G 681 ASN G 688 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18279 Z= 0.219 Angle : 0.486 10.056 24716 Z= 0.258 Chirality : 0.042 0.347 2931 Planarity : 0.003 0.040 3023 Dihedral : 7.194 59.535 2367 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.04 % Allowed : 12.77 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.25 (0.19), residues: 2146 helix: 3.37 (0.14), residues: 1202 sheet: 0.51 (0.27), residues: 329 loop : 0.60 (0.29), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 304 HIS 0.005 0.001 HIS F 684 PHE 0.022 0.002 PHE G 574 TYR 0.009 0.001 TYR B 740 ARG 0.005 0.000 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 518 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7781 (tttm) cc_final: 0.7485 (tttm) REVERT: B 669 LYS cc_start: 0.8454 (mtpm) cc_final: 0.8199 (ttmm) REVERT: C 301 PHE cc_start: 0.6619 (t80) cc_final: 0.6230 (t80) REVERT: C 669 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7935 (mttm) REVERT: D 531 GLN cc_start: 0.7109 (mt0) cc_final: 0.6864 (mt0) REVERT: D 664 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7518 (mttm) REVERT: F 692 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8039 (mtmt) REVERT: F 717 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7628 (tp30) REVERT: G 324 LYS cc_start: 0.8528 (mttm) cc_final: 0.8290 (mttm) REVERT: G 689 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7941 (ttp) outliers start: 61 outliers final: 32 residues processed: 529 average time/residue: 1.3283 time to fit residues: 787.0857 Evaluate side-chains 548 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 513 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 692 LYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 689 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 0.0060 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN D 576 ASN E 531 GLN E 648 GLN ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18279 Z= 0.175 Angle : 0.447 9.898 24716 Z= 0.239 Chirality : 0.041 0.166 2931 Planarity : 0.003 0.036 3023 Dihedral : 6.949 58.412 2367 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.04 % Allowed : 13.47 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.35 (0.19), residues: 2146 helix: 3.51 (0.14), residues: 1202 sheet: 0.48 (0.27), residues: 329 loop : 0.57 (0.29), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 304 HIS 0.004 0.001 HIS E 708 PHE 0.020 0.001 PHE D 301 TYR 0.008 0.001 TYR E 740 ARG 0.004 0.000 ARG E 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 506 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7725 (tttm) cc_final: 0.7525 (tttm) REVERT: A 737 ASP cc_start: 0.7713 (t0) cc_final: 0.7436 (t0) REVERT: B 629 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7760 (t80) REVERT: B 669 LYS cc_start: 0.8476 (mtpm) cc_final: 0.8238 (ttmm) REVERT: B 673 LYS cc_start: 0.8749 (tttm) cc_final: 0.8530 (tttm) REVERT: C 301 PHE cc_start: 0.6582 (t80) cc_final: 0.6202 (t80) REVERT: C 532 LEU cc_start: 0.8453 (tp) cc_final: 0.8251 (tt) REVERT: D 531 GLN cc_start: 0.7097 (mt0) cc_final: 0.6804 (mt0) REVERT: D 664 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7449 (mttt) REVERT: F 612 MET cc_start: 0.8400 (mtp) cc_final: 0.8125 (ttm) REVERT: F 692 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8039 (mtmt) REVERT: F 717 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7549 (tp30) REVERT: G 324 LYS cc_start: 0.8523 (mttm) cc_final: 0.8299 (mttm) REVERT: G 689 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7931 (ttp) outliers start: 61 outliers final: 31 residues processed: 521 average time/residue: 1.2722 time to fit residues: 738.7019 Evaluate side-chains 546 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 511 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 701 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 692 LYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 689 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 8.9990 chunk 188 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 209 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 688 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 291 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18279 Z= 0.244 Angle : 0.486 8.730 24716 Z= 0.257 Chirality : 0.042 0.193 2931 Planarity : 0.003 0.038 3023 Dihedral : 7.037 59.436 2365 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.34 % Allowed : 13.97 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.28 (0.19), residues: 2146 helix: 3.50 (0.14), residues: 1202 sheet: 0.30 (0.29), residues: 311 loop : 0.52 (0.28), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 304 HIS 0.005 0.001 HIS F 684 PHE 0.019 0.002 PHE F 715 TYR 0.016 0.002 TYR D 740 ARG 0.003 0.000 ARG E 671 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 517 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7779 (tttm) cc_final: 0.7534 (tttm) REVERT: A 737 ASP cc_start: 0.7728 (t0) cc_final: 0.7354 (t0) REVERT: B 629 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.8031 (t80) REVERT: B 669 LYS cc_start: 0.8504 (mtpm) cc_final: 0.8246 (ttmm) REVERT: C 301 PHE cc_start: 0.6580 (t80) cc_final: 0.6223 (t80) REVERT: D 531 GLN cc_start: 0.7143 (mt0) cc_final: 0.6881 (mt0) REVERT: D 664 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7418 (mttt) REVERT: E 737 ASP cc_start: 0.7021 (t0) cc_final: 0.6762 (t0) REVERT: F 692 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8058 (mtmt) REVERT: F 717 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7482 (tp30) REVERT: G 689 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7941 (ttp) outliers start: 67 outliers final: 36 residues processed: 534 average time/residue: 1.2930 time to fit residues: 769.3421 Evaluate side-chains 551 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 511 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 692 LYS Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 689 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN B 613 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 648 GLN F 688 ASN G 291 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 ASN G 681 ASN G 698 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18279 Z= 0.307 Angle : 0.508 8.920 24716 Z= 0.268 Chirality : 0.042 0.168 2931 Planarity : 0.003 0.037 3023 Dihedral : 7.186 59.672 2365 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.34 % Allowed : 14.46 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.14 (0.19), residues: 2146 helix: 3.43 (0.14), residues: 1202 sheet: 0.20 (0.29), residues: 311 loop : 0.39 (0.28), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 304 HIS 0.007 0.001 HIS E 708 PHE 0.022 0.002 PHE F 715 TYR 0.016 0.002 TYR D 740 ARG 0.002 0.000 ARG E 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 507 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 737 ASP cc_start: 0.7738 (t0) cc_final: 0.7384 (t0) REVERT: B 629 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.8030 (t80) REVERT: B 669 LYS cc_start: 0.8469 (mtpm) cc_final: 0.8208 (ttmm) REVERT: C 301 PHE cc_start: 0.6591 (t80) cc_final: 0.6252 (t80) REVERT: D 531 GLN cc_start: 0.7177 (mt0) cc_final: 0.6928 (mt0) REVERT: D 664 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7072 (mptm) REVERT: F 692 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8104 (mtmt) REVERT: F 717 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7482 (tp30) REVERT: G 599 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7949 (ttm-80) outliers start: 67 outliers final: 44 residues processed: 526 average time/residue: 1.3086 time to fit residues: 764.8346 Evaluate side-chains 551 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 503 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 534 LYS Chi-restraints excluded: chain F residue 576 ASN Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 680 LEU Chi-restraints excluded: chain F residue 692 LYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 599 ARG Chi-restraints excluded: chain G residue 697 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 20.0000 chunk 83 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN F 531 GLN G 291 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18279 Z= 0.234 Angle : 0.492 9.087 24716 Z= 0.259 Chirality : 0.041 0.185 2931 Planarity : 0.003 0.036 3023 Dihedral : 7.105 59.146 2365 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.04 % Allowed : 14.76 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.19 (0.19), residues: 2146 helix: 3.49 (0.14), residues: 1202 sheet: 0.12 (0.29), residues: 311 loop : 0.42 (0.28), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 304 HIS 0.005 0.001 HIS E 708 PHE 0.019 0.001 PHE A 574 TYR 0.016 0.001 TYR D 740 ARG 0.001 0.000 ARG G 722 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 507 time to evaluate : 2.102 Fit side-chains revert: symmetry clash REVERT: A 737 ASP cc_start: 0.7735 (t0) cc_final: 0.7336 (t0) REVERT: B 629 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.8030 (t80) REVERT: B 669 LYS cc_start: 0.8458 (mtpm) cc_final: 0.8201 (ttmm) REVERT: B 731 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8403 (ttpp) REVERT: C 301 PHE cc_start: 0.6585 (t80) cc_final: 0.6237 (t80) REVERT: C 526 LYS cc_start: 0.7096 (mttt) cc_final: 0.6817 (mttt) REVERT: D 531 GLN cc_start: 0.7160 (mt0) cc_final: 0.6904 (mt0) REVERT: D 664 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7398 (mttt) REVERT: F 692 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8085 (mtmt) REVERT: F 717 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7438 (tp30) outliers start: 61 outliers final: 43 residues processed: 529 average time/residue: 1.3039 time to fit residues: 766.2762 Evaluate side-chains 547 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 501 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 701 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 534 LYS Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 692 LYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 176 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 531 GLN F 688 ASN G 291 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18279 Z= 0.195 Angle : 0.473 9.101 24716 Z= 0.249 Chirality : 0.041 0.187 2931 Planarity : 0.003 0.036 3023 Dihedral : 6.973 58.626 2365 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.74 % Allowed : 15.46 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.26 (0.19), residues: 2146 helix: 3.56 (0.14), residues: 1202 sheet: 0.17 (0.29), residues: 305 loop : 0.41 (0.28), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 304 HIS 0.004 0.001 HIS E 708 PHE 0.019 0.001 PHE D 301 TYR 0.014 0.001 TYR D 740 ARG 0.004 0.000 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 502 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: A 737 ASP cc_start: 0.7719 (t0) cc_final: 0.7284 (t0) REVERT: B 629 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.8019 (t80) REVERT: B 669 LYS cc_start: 0.8484 (mtpm) cc_final: 0.8243 (ttmm) REVERT: B 731 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8397 (ttpp) REVERT: C 301 PHE cc_start: 0.6546 (t80) cc_final: 0.6224 (t80) REVERT: C 689 MET cc_start: 0.8410 (ttp) cc_final: 0.8149 (ttp) REVERT: D 531 GLN cc_start: 0.7143 (mt0) cc_final: 0.6890 (mt0) REVERT: D 664 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7423 (mttt) REVERT: F 692 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8083 (mtmt) REVERT: F 717 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7395 (tp30) outliers start: 55 outliers final: 41 residues processed: 517 average time/residue: 1.2942 time to fit residues: 742.9691 Evaluate side-chains 542 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 498 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 701 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 692 LYS Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.0970 chunk 125 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 172 optimal weight: 0.0020 chunk 17 optimal weight: 0.3980 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN F 681 ASN G 291 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18279 Z= 0.156 Angle : 0.465 10.091 24716 Z= 0.245 Chirality : 0.040 0.194 2931 Planarity : 0.003 0.035 3023 Dihedral : 6.835 58.476 2365 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.19 % Allowed : 16.41 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.32 (0.19), residues: 2146 helix: 3.61 (0.14), residues: 1202 sheet: 0.14 (0.29), residues: 305 loop : 0.45 (0.28), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 304 HIS 0.004 0.001 HIS E 708 PHE 0.020 0.001 PHE D 301 TYR 0.013 0.001 TYR D 740 ARG 0.002 0.000 ARG E 671 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 512 time to evaluate : 2.125 Fit side-chains revert: symmetry clash REVERT: A 737 ASP cc_start: 0.7703 (t0) cc_final: 0.7269 (t0) REVERT: B 629 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.8018 (t80) REVERT: B 669 LYS cc_start: 0.8481 (mtpm) cc_final: 0.8228 (ttmm) REVERT: B 731 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8405 (ttpp) REVERT: C 301 PHE cc_start: 0.6550 (t80) cc_final: 0.6224 (t80) REVERT: C 689 MET cc_start: 0.8417 (ttp) cc_final: 0.8158 (ttp) REVERT: D 531 GLN cc_start: 0.7111 (mt0) cc_final: 0.6854 (mt0) REVERT: D 664 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7406 (mttt) REVERT: E 739 LYS cc_start: 0.8296 (mttp) cc_final: 0.8063 (mttp) REVERT: F 717 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7288 (tp30) outliers start: 44 outliers final: 37 residues processed: 524 average time/residue: 1.2986 time to fit residues: 757.2432 Evaluate side-chains 543 residues out of total 2005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 504 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 701 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 531 GLN F 688 ASN G 291 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.163746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128039 restraints weight = 25253.918| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.73 r_work: 0.3409 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18279 Z= 0.246 Angle : 0.499 10.731 24716 Z= 0.262 Chirality : 0.042 0.188 2931 Planarity : 0.003 0.035 3023 Dihedral : 6.850 58.772 2365 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.39 % Allowed : 16.66 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.22 (0.19), residues: 2146 helix: 3.55 (0.14), residues: 1202 sheet: 0.05 (0.28), residues: 311 loop : 0.40 (0.28), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 683 HIS 0.005 0.001 HIS E 708 PHE 0.020 0.001 PHE D 301 TYR 0.014 0.001 TYR D 740 ARG 0.002 0.000 ARG E 644 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10483.40 seconds wall clock time: 182 minutes 39.11 seconds (10959.11 seconds total)