Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 23:02:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/04_2023/7dtu_30854.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/04_2023/7dtu_30854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/04_2023/7dtu_30854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/04_2023/7dtu_30854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/04_2023/7dtu_30854.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/04_2023/7dtu_30854.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 6808 2.51 5 N 1894 2.21 5 O 2098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10846 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5310 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 29, 'TRANS': 748} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 938 Unresolved non-hydrogen angles: 1205 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 36, 'GLU:plan': 22, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 522 Chain: "B" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5310 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 29, 'TRANS': 748} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 938 Unresolved non-hydrogen angles: 1205 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 36, 'GLU:plan': 22, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 522 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.27, per 1000 atoms: 0.58 Number of scatterers: 10846 At special positions: 0 Unit cell: (95.95, 102.01, 181.8, 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 46 16.00 O 2098 8.00 N 1894 7.00 C 6808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.04 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=1.41 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.04 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.02 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=1.42 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.04 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.02 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1102 " - " ASN A 287 " " NAG A1103 " - " ASN A 446 " " NAG A1104 " - " ASN A 468 " " NAG B1102 " - " ASN B 287 " " NAG B1103 " - " ASN B 446 " " NAG B1104 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 1.8 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 48.1% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.727A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 4.429A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.895A pdb=" N ASP A 121 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.655A pdb=" N ASN A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 removed outlier: 3.989A pdb=" N ASN A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.960A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.094A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.504A pdb=" N SER A 342 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.467A pdb=" N GLU A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.790A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.786A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.749A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.151A pdb=" N LYS A 527 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.902A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 removed outlier: 4.564A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 removed outlier: 3.875A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 681 through 691 removed outlier: 4.019A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 728 through 746 removed outlier: 4.309A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 792 removed outlier: 4.442A pdb=" N CYS A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 785 " --> pdb=" O CYS A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.791A pdb=" N LYS A 796 " --> pdb=" O LYS A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 827 removed outlier: 4.110A pdb=" N ILE A 822 " --> pdb=" O TRP A 818 " (cutoff:3.500A) Proline residue: A 823 - end of helix Processing helix chain 'A' and resid 829 through 858 removed outlier: 4.056A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL A 836 " --> pdb=" O PHE A 832 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.726A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 4.428A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 122 removed outlier: 3.895A pdb=" N ASP B 121 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.655A pdb=" N ASN B 130 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 removed outlier: 3.989A pdb=" N ASN B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.960A pdb=" N ILE B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.095A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 338 through 342 removed outlier: 3.504A pdb=" N SER B 342 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 4.467A pdb=" N GLU B 350 " --> pdb=" O GLY B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.789A pdb=" N SER B 403 " --> pdb=" O ASN B 400 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 404 " --> pdb=" O ILE B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 404' Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.785A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.748A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 removed outlier: 4.151A pdb=" N LYS B 527 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.902A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 665 removed outlier: 4.564A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 669 removed outlier: 3.874A pdb=" N ILE B 669 " --> pdb=" O LEU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 681 through 691 removed outlier: 4.020A pdb=" N SER B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 728 through 746 removed outlier: 4.310A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR B 744 " --> pdb=" O VAL B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 792 removed outlier: 4.442A pdb=" N CYS B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU B 782 " --> pdb=" O GLY B 778 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 785 " --> pdb=" O CYS B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 797 removed outlier: 3.791A pdb=" N LYS B 796 " --> pdb=" O LYS B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 827 removed outlier: 4.111A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 829 through 858 removed outlier: 4.057A pdb=" N SER B 834 " --> pdb=" O GLY B 830 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 836 " --> pdb=" O PHE B 832 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 837 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.647A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.705A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.516A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 210 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 268 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 214 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.716A pdb=" N GLY A 319 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 321 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 522 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 468 through 470 removed outlier: 3.652A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.648A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA9, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.705A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.517A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 210 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 268 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 214 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.716A pdb=" N GLY B 319 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 321 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 522 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 468 through 470 removed outlier: 3.652A pdb=" N PHE B 469 " --> pdb=" O VAL B 477 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1398 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: 3.48 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3605 1.34 - 1.46: 2471 1.46 - 1.58: 4916 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 11046 Sorted by residual: bond pdb=" C1 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1 NAG A1103 " pdb=" O5 NAG A1103 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 NAG A1102 " pdb=" O5 NAG A1102 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C1 NAG B1102 " pdb=" O5 NAG B1102 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG B1104 " pdb=" O5 NAG B1104 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 11041 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.41: 256 106.41 - 113.32: 6103 113.32 - 120.23: 3909 120.23 - 127.13: 4718 127.13 - 134.04: 116 Bond angle restraints: 15102 Sorted by residual: angle pdb=" CA TYR A 573 " pdb=" CB TYR A 573 " pdb=" CG TYR A 573 " ideal model delta sigma weight residual 113.90 120.59 -6.69 1.80e+00 3.09e-01 1.38e+01 angle pdb=" CA TYR B 573 " pdb=" CB TYR B 573 " pdb=" CG TYR B 573 " ideal model delta sigma weight residual 113.90 120.51 -6.61 1.80e+00 3.09e-01 1.35e+01 angle pdb=" C GLU B 572 " pdb=" N TYR B 573 " pdb=" CA TYR B 573 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C GLU A 572 " pdb=" N TYR A 573 " pdb=" CA TYR A 573 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C CYS A 101 " pdb=" N ASN A 102 " pdb=" CA ASN A 102 " ideal model delta sigma weight residual 122.40 127.67 -5.27 1.45e+00 4.76e-01 1.32e+01 ... (remaining 15097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5836 17.94 - 35.88: 469 35.88 - 53.82: 75 53.82 - 71.76: 16 71.76 - 89.70: 16 Dihedral angle restraints: 6412 sinusoidal: 1898 harmonic: 4514 Sorted by residual: dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual 93.00 164.95 -71.95 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 164.94 -71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 568 " pdb=" SG CYS A 568 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 160.35 -67.35 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 6409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1249 0.051 - 0.102: 406 0.102 - 0.152: 121 0.152 - 0.203: 16 0.203 - 0.254: 8 Chirality restraints: 1800 Sorted by residual: chirality pdb=" CG LEU B 37 " pdb=" CB LEU B 37 " pdb=" CD1 LEU B 37 " pdb=" CD2 LEU B 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU A 37 " pdb=" CB LEU A 37 " pdb=" CD1 LEU A 37 " pdb=" CD2 LEU A 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1 NAG A1104 " pdb=" ND2 ASN A 468 " pdb=" C2 NAG A1104 " pdb=" O5 NAG A1104 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1797 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 445 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C THR B 445 " -0.039 2.00e-02 2.50e+03 pdb=" O THR B 445 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 446 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 445 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C THR A 445 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 445 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 446 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 585 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 586 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 586 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 586 " 0.028 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3299 2.80 - 3.33: 10444 3.33 - 3.85: 19032 3.85 - 4.38: 20463 4.38 - 4.90: 33105 Nonbonded interactions: 86343 Sorted by model distance: nonbonded pdb=" O SER B 171 " pdb=" NH2 ARG B 185 " model vdw 2.277 2.520 nonbonded pdb=" O SER A 171 " pdb=" NH2 ARG A 185 " model vdw 2.277 2.520 nonbonded pdb=" O GLU A 525 " pdb=" NH2 ARG A 535 " model vdw 2.299 2.520 nonbonded pdb=" O GLU B 525 " pdb=" NH2 ARG B 535 " model vdw 2.299 2.520 nonbonded pdb=" OH TYR A 203 " pdb=" OE1 GLU A 525 " model vdw 2.315 2.440 ... (remaining 86338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.450 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 31.680 Find NCS groups from input model: 0.600 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.006 0.070 11046 Z= 0.398 Angle : 0.903 8.278 15102 Z= 0.514 Chirality : 0.056 0.254 1800 Planarity : 0.005 0.051 1984 Dihedral : 14.571 89.703 3430 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer Outliers : 0.00 % 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: -3.95 (0.18), residues: 1540 helix: -2.02 (0.15), residues: 606 sheet: -3.70 (0.29), residues: 210 loop : -2.74 (0.21), residues: 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.332 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1816 time to fit residues: 6.3831 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.4980 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 50.0000 chunk 39 optimal weight: 0.0000 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 0.0870 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 245 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 326 GLN A 419 ASN A 429 HIS A 432 GLN A 463 HIS B 72 GLN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 245 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS B 419 ASN B 429 HIS B 432 GLN B 463 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 11046 Z= 0.161 Angle : 0.565 7.815 15102 Z= 0.305 Chirality : 0.045 0.310 1800 Planarity : 0.003 0.038 1984 Dihedral : 5.563 20.303 1630 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 0.00 % 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: -2.50 (0.21), residues: 1540 helix: -0.37 (0.19), residues: 610 sheet: -3.23 (0.32), residues: 202 loop : -2.31 (0.23), residues: 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 1.357 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1726 time to fit residues: 6.8853 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 116 optimal weight: 0.0770 chunk 95 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 40.0000 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 40.0000 chunk 47 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN B 466 HIS ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 11046 Z= 0.384 Angle : 0.674 8.072 15102 Z= 0.366 Chirality : 0.046 0.271 1800 Planarity : 0.004 0.036 1984 Dihedral : 5.468 25.827 1630 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer Outliers : 0.00 % 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: -1.99 (0.21), residues: 1540 helix: 0.29 (0.20), residues: 622 sheet: -3.11 (0.34), residues: 198 loop : -2.25 (0.23), residues: 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.401 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1717 time to fit residues: 6.2735 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 50.0000 chunk 105 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 94 optimal weight: 0.9990 chunk 140 optimal weight: 0.4980 chunk 148 optimal weight: 50.0000 chunk 73 optimal weight: 10.0000 chunk 133 optimal weight: 50.0000 chunk 40 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11046 Z= 0.172 Angle : 0.540 7.501 15102 Z= 0.288 Chirality : 0.044 0.273 1800 Planarity : 0.003 0.034 1984 Dihedral : 4.960 24.513 1630 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 0.00 % 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: -1.50 (0.22), residues: 1540 helix: 0.88 (0.21), residues: 616 sheet: -2.97 (0.35), residues: 188 loop : -2.15 (0.23), residues: 736 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1786 time to fit residues: 7.1088 Evaluate side-chains 16 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.0970 chunk 84 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 110 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 30.0000 chunk 133 optimal weight: 50.0000 chunk 37 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS A 361 GLN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 11046 Z= 0.130 Angle : 0.513 7.240 15102 Z= 0.269 Chirality : 0.044 0.286 1800 Planarity : 0.003 0.033 1984 Dihedral : 4.618 20.696 1630 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 0.00 % 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: -1.04 (0.22), residues: 1540 helix: 1.21 (0.21), residues: 620 sheet: -2.33 (0.39), residues: 164 loop : -2.01 (0.24), residues: 756 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2043 time to fit residues: 7.7242 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 9.9990 chunk 134 optimal weight: 40.0000 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 30.0000 chunk 78 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 11046 Z= 0.368 Angle : 0.642 8.327 15102 Z= 0.347 Chirality : 0.045 0.269 1800 Planarity : 0.004 0.036 1984 Dihedral : 4.941 26.551 1630 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 0.00 % 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: -1.20 (0.22), residues: 1540 helix: 1.19 (0.21), residues: 620 sheet: -2.81 (0.34), residues: 204 loop : -2.01 (0.24), residues: 716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.452 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1690 time to fit residues: 6.2019 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 40.0000 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 108 optimal weight: 0.0000 chunk 125 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 148 optimal weight: 50.0000 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 50.0000 chunk 91 optimal weight: 0.9980 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11046 Z= 0.184 Angle : 0.540 8.304 15102 Z= 0.285 Chirality : 0.044 0.265 1800 Planarity : 0.003 0.033 1984 Dihedral : 4.691 25.618 1630 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 0.00 % 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: -0.81 (0.22), residues: 1540 helix: 1.50 (0.21), residues: 620 sheet: -2.18 (0.37), residues: 180 loop : -1.96 (0.24), residues: 740 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1649 time to fit residues: 5.9768 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 11046 Z= 0.277 Angle : 0.590 8.905 15102 Z= 0.316 Chirality : 0.045 0.263 1800 Planarity : 0.004 0.033 1984 Dihedral : 4.785 28.071 1630 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer Outliers : 0.00 % 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: -0.86 (0.22), residues: 1540 helix: 1.56 (0.21), residues: 618 sheet: -2.68 (0.35), residues: 194 loop : -1.90 (0.24), residues: 728 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.354 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1672 time to fit residues: 6.2326 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 30.0000 chunk 137 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 11046 Z= 0.251 Angle : 0.576 8.663 15102 Z= 0.307 Chirality : 0.045 0.264 1800 Planarity : 0.004 0.033 1984 Dihedral : 4.780 28.850 1630 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer Outliers : 0.00 % 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: -0.83 (0.22), residues: 1540 helix: 1.45 (0.21), residues: 638 sheet: -2.10 (0.38), residues: 170 loop : -2.07 (0.23), residues: 732 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1700 time to fit residues: 6.4751 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 141 optimal weight: 50.0000 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 40.0000 chunk 97 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 11046 Z= 0.303 Angle : 0.617 9.429 15102 Z= 0.330 Chirality : 0.045 0.255 1800 Planarity : 0.004 0.034 1984 Dihedral : 4.955 30.715 1630 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer Outliers : 0.00 % 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: -0.95 (0.22), residues: 1540 helix: 1.40 (0.21), residues: 636 sheet: -2.25 (0.36), residues: 180 loop : -2.15 (0.23), residues: 724 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1617 time to fit residues: 6.0688 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.034311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.027443 restraints weight = 144923.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.027971 restraints weight = 99970.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028345 restraints weight = 75972.768| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11046 Z= 0.165 Angle : 0.538 9.421 15102 Z= 0.283 Chirality : 0.045 0.262 1800 Planarity : 0.003 0.033 1984 Dihedral : 4.628 26.560 1630 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 0.00 % 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: -0.70 (0.22), residues: 1540 helix: 1.55 (0.21), residues: 650 sheet: -2.16 (0.36), residues: 180 loop : -1.99 (0.24), residues: 710 =============================================================================== Job complete usr+sys time: 1462.31 seconds wall clock time: 28 minutes 7.51 seconds (1687.51 seconds total)