Starting phenix.real_space_refine on Fri Jan 19 08:23:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/01_2024/7dtu_30854.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/01_2024/7dtu_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_30854/01_2024/7dtu_30854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/01_2024/7dtu_30854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/01_2024/7dtu_30854.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dtu_30854/01_2024/7dtu_30854.pdb" } resolution = 4.4 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= 0.000 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.86, per 1000 atoms: 0.63 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: 4.56 Conformation dependent library (CDL) restraints added in 2.3 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: 1.18 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: 3.49 Time building geometry restraints manager: 5.06 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: 6090 17.94 - 35.88: 485 35.88 - 53.82: 91 53.82 - 71.76: 24 71.76 - 89.70: 16 Dihedral angle restraints: 6706 sinusoidal: 2192 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 6703 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.870 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 32.880 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.060 ------------------------------------------------------------------------------- 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 : 14.686 89.703 3724 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 % Allowed : 11.94 % Favored : 88.06 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 458 HIS 0.005 0.001 HIS B 429 PHE 0.024 0.002 PHE B 270 TYR 0.023 0.003 TYR B 573 ARG 0.007 0.001 ARG A 69 *********************** 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 : 1.245 Fit side-chains REVERT: A 473 MET cc_start: 0.7651 (ptp) cc_final: 0.6859 (mpp) REVERT: B 473 MET cc_start: 0.7586 (ptp) cc_final: 0.6812 (mpp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1795 time to fit residues: 6.3341 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11046 Z= 0.154 Angle : 0.553 7.793 15102 Z= 0.299 Chirality : 0.045 0.299 1800 Planarity : 0.003 0.036 1984 Dihedral : 7.207 57.484 1924 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: -2.45 (0.21), residues: 1540 helix: -0.30 (0.19), residues: 610 sheet: -3.24 (0.35), residues: 182 loop : -2.34 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 208 HIS 0.003 0.001 HIS A 463 PHE 0.010 0.001 PHE B 270 TYR 0.018 0.002 TYR B 573 ARG 0.002 0.000 ARG B 205 *********************** 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 : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 464 LEU cc_start: 0.9446 (mt) cc_final: 0.9121 (mt) REVERT: A 473 MET cc_start: 0.7394 (ptp) cc_final: 0.6784 (mpp) REVERT: B 464 LEU cc_start: 0.9449 (mt) cc_final: 0.9109 (mt) REVERT: B 473 MET cc_start: 0.7425 (ptp) cc_final: 0.6683 (mpp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1615 time to fit residues: 6.3213 Evaluate side-chains 16 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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: 8.9990 chunk 43 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 140 optimal weight: 40.0000 chunk 151 optimal weight: 40.0000 chunk 124 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN A 466 HIS ** 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 466 HIS ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1472 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= 0.339 Angle : 0.641 7.507 15102 Z= 0.348 Chirality : 0.045 0.271 1800 Planarity : 0.004 0.035 1984 Dihedral : 6.980 54.461 1924 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % 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: -1.89 (0.21), residues: 1540 helix: 0.41 (0.20), residues: 616 sheet: -3.07 (0.34), residues: 198 loop : -2.21 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 458 HIS 0.004 0.001 HIS B 192 PHE 0.020 0.002 PHE A 38 TYR 0.017 0.002 TYR B 573 ARG 0.005 0.001 ARG A 69 *********************** 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 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.255 Fit side-chains REVERT: A 197 MET cc_start: 0.9133 (mtm) cc_final: 0.8592 (mtp) REVERT: A 307 MET cc_start: 0.8415 (mmp) cc_final: 0.8213 (mmm) REVERT: B 197 MET cc_start: 0.9155 (mtm) cc_final: 0.8592 (mtp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1692 time to fit residues: 5.4935 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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: 0.6980 chunk 105 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 40.0000 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 0.0770 chunk 148 optimal weight: 50.0000 chunk 73 optimal weight: 8.9990 chunk 133 optimal weight: 50.0000 chunk 40 optimal weight: 7.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- 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: 0.7960 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11046 Z= 0.172 Angle : 0.530 7.403 15102 Z= 0.284 Chirality : 0.044 0.264 1800 Planarity : 0.003 0.034 1984 Dihedral : 6.156 51.096 1924 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -1.39 (0.22), residues: 1540 helix: 0.97 (0.21), residues: 616 sheet: -2.83 (0.35), residues: 194 loop : -2.09 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 352 HIS 0.002 0.000 HIS A 429 PHE 0.010 0.001 PHE A 38 TYR 0.016 0.002 TYR A 573 ARG 0.003 0.000 ARG A 69 *********************** 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 17 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9198 (mtm) cc_final: 0.8682 (mtp) REVERT: B 197 MET cc_start: 0.9231 (mtm) cc_final: 0.8699 (mtp) REVERT: B 307 MET cc_start: 0.8078 (mmp) cc_final: 0.7845 (mmm) REVERT: B 464 LEU cc_start: 0.9481 (mt) cc_final: 0.9143 (mt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1776 time to fit residues: 6.3821 Evaluate side-chains 17 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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: 6.9990 chunk 84 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 0.0040 chunk 61 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 40.0000 chunk 133 optimal weight: 50.0000 chunk 37 optimal weight: 4.9990 overall best weight: 3.3598 ------------------------------------------------------------------------------- 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 359 HIS A 361 GLN ** 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 359 HIS B 361 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11046 Z= 0.228 Angle : 0.549 7.884 15102 Z= 0.296 Chirality : 0.044 0.270 1800 Planarity : 0.003 0.033 1984 Dihedral : 6.074 51.308 1924 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: -1.19 (0.22), residues: 1540 helix: 1.20 (0.21), residues: 620 sheet: -2.85 (0.33), residues: 204 loop : -1.99 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 458 HIS 0.002 0.001 HIS B 192 PHE 0.012 0.001 PHE A 38 TYR 0.016 0.002 TYR A 573 ARG 0.004 0.000 ARG A 69 *********************** 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 16 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.276 Fit side-chains REVERT: A 197 MET cc_start: 0.9209 (mtm) cc_final: 0.8610 (mtp) REVERT: B 197 MET cc_start: 0.9231 (mtm) cc_final: 0.8638 (mtp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1732 time to fit residues: 6.1382 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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: 0.0370 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- 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: 0.8015 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11046 Z= 0.292 Angle : 0.595 8.069 15102 Z= 0.321 Chirality : 0.045 0.259 1800 Planarity : 0.004 0.034 1984 Dihedral : 6.278 49.708 1924 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: -1.07 (0.22), residues: 1540 helix: 1.28 (0.21), residues: 620 sheet: -2.26 (0.38), residues: 170 loop : -2.13 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 458 HIS 0.002 0.001 HIS B 359 PHE 0.015 0.002 PHE B 270 TYR 0.015 0.002 TYR B 573 ARG 0.005 0.000 ARG B 69 *********************** 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 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9116 (mtm) cc_final: 0.8591 (mtp) REVERT: B 197 MET cc_start: 0.9122 (mtm) cc_final: 0.8574 (mtp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1631 time to fit residues: 5.3761 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 148 optimal weight: 50.0000 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11046 Z= 0.224 Angle : 0.550 7.226 15102 Z= 0.295 Chirality : 0.044 0.253 1800 Planarity : 0.003 0.034 1984 Dihedral : 6.045 48.042 1924 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 1.52 (0.21), residues: 620 sheet: -2.20 (0.38), residues: 170 loop : -1.99 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 352 HIS 0.002 0.001 HIS A 463 PHE 0.011 0.001 PHE B 589 TYR 0.016 0.002 TYR A 573 ARG 0.004 0.000 ARG B 69 *********************** 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 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.290 Fit side-chains REVERT: A 197 MET cc_start: 0.9068 (mtm) cc_final: 0.8527 (mtp) REVERT: A 473 MET cc_start: 0.7559 (mtt) cc_final: 0.6595 (mpp) REVERT: B 197 MET cc_start: 0.9100 (mtm) cc_final: 0.8547 (mtp) REVERT: B 473 MET cc_start: 0.7639 (mtt) cc_final: 0.6665 (mpp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1649 time to fit residues: 5.4203 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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: 20.0000 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.7997 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11046 Z= 0.229 Angle : 0.553 7.571 15102 Z= 0.296 Chirality : 0.044 0.257 1800 Planarity : 0.003 0.033 1984 Dihedral : 6.012 47.903 1924 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -0.72 (0.23), residues: 1540 helix: 1.59 (0.21), residues: 620 sheet: -2.20 (0.38), residues: 170 loop : -1.93 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 352 HIS 0.002 0.001 HIS A 192 PHE 0.012 0.001 PHE A 589 TYR 0.014 0.002 TYR B 573 ARG 0.005 0.000 ARG A 69 *********************** 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 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9075 (mtm) cc_final: 0.8513 (mtp) REVERT: B 197 MET cc_start: 0.9106 (mtm) cc_final: 0.8535 (mtp) REVERT: B 473 MET cc_start: 0.7649 (mtt) cc_final: 0.6675 (mpp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1670 time to fit residues: 5.4336 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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: 20.0000 chunk 138 optimal weight: 10.0000 chunk 83 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 137 optimal weight: 0.0270 chunk 90 optimal weight: 3.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- 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: 0.7949 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11046 Z= 0.139 Angle : 0.522 8.777 15102 Z= 0.272 Chirality : 0.044 0.261 1800 Planarity : 0.003 0.033 1984 Dihedral : 5.594 47.500 1924 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.63 (0.23), residues: 1540 helix: 1.61 (0.21), residues: 632 sheet: -2.15 (0.37), residues: 180 loop : -1.85 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 352 HIS 0.001 0.000 HIS B 192 PHE 0.007 0.001 PHE A 589 TYR 0.015 0.001 TYR A 573 ARG 0.004 0.000 ARG A 69 *********************** 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 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.276 Fit side-chains REVERT: A 197 MET cc_start: 0.9085 (mtm) cc_final: 0.8578 (mtp) REVERT: A 473 MET cc_start: 0.7377 (mtt) cc_final: 0.6416 (mpp) REVERT: B 197 MET cc_start: 0.9097 (mtm) cc_final: 0.8589 (mtp) REVERT: B 473 MET cc_start: 0.7461 (mtt) cc_final: 0.6480 (mpp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1624 time to fit residues: 5.3895 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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: 8.9990 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 101 optimal weight: 0.4980 chunk 153 optimal weight: 9.9990 chunk 141 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 40.0000 chunk 97 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11046 Z= 0.191 Angle : 0.523 7.948 15102 Z= 0.279 Chirality : 0.044 0.263 1800 Planarity : 0.003 0.031 1984 Dihedral : 5.580 48.420 1924 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.56 (0.23), residues: 1540 helix: 1.72 (0.21), residues: 630 sheet: -2.17 (0.37), residues: 180 loop : -1.85 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 352 HIS 0.002 0.001 HIS A 192 PHE 0.012 0.001 PHE A 38 TYR 0.015 0.001 TYR A 573 ARG 0.004 0.000 ARG A 69 ********************** 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 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.142 Fit side-chains REVERT: A 197 MET cc_start: 0.9068 (mtm) cc_final: 0.8551 (mtp) REVERT: A 473 MET cc_start: 0.7531 (mtt) cc_final: 0.6505 (mpp) REVERT: B 197 MET cc_start: 0.9078 (mtm) cc_final: 0.8529 (mtp) REVERT: B 473 MET cc_start: 0.7499 (mtt) cc_final: 0.6561 (mpp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1573 time to fit residues: 5.4156 Evaluate side-chains 14 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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: 8.9990 chunk 37 optimal weight: 0.0060 chunk 112 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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** ** 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 = 0.3133 r_free = 0.3133 target = 0.034678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.027817 restraints weight = 144422.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.028321 restraints weight = 100588.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.028695 restraints weight = 77127.421| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11046 Z= 0.142 Angle : 0.505 7.741 15102 Z= 0.265 Chirality : 0.044 0.266 1800 Planarity : 0.003 0.032 1984 Dihedral : 5.284 47.805 1924 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.40 (0.23), residues: 1540 helix: 1.79 (0.21), residues: 644 sheet: -2.10 (0.37), residues: 180 loop : -1.77 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 352 HIS 0.001 0.000 HIS B 192 PHE 0.006 0.001 PHE B 589 TYR 0.016 0.001 TYR A 573 ARG 0.004 0.000 ARG A 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1570.37 seconds wall clock time: 29 minutes 50.30 seconds (1790.30 seconds total)