Starting phenix.real_space_refine on Sun Mar 17 06:17:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/03_2024/3j9p_6267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/03_2024/3j9p_6267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/03_2024/3j9p_6267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/03_2024/3j9p_6267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/03_2024/3j9p_6267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/03_2024/3j9p_6267.pdb" } resolution = 4.24 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 ------------------------------------------------------------------------------- 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= 1.000 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 120 5.16 5 C 11100 2.51 5 N 2844 2.21 5 O 2888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 592": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "D ARG 852": "NH1" <-> "NH2" Residue "D GLU 1041": "OE1" <-> "OE2" Residue "D GLU 1063": "OE1" <-> "OE2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A GLU 1063": "OE1" <-> "OE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B GLU 1063": "OE1" <-> "OE2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "C GLU 1041": "OE1" <-> "OE2" Residue "C GLU 1063": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16952 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4238 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 22, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 519} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4238 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 22, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 519} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "B" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4238 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 22, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 519} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Chain: "C" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4238 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 22, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 519} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Time building chain proxies: 8.60, per 1000 atoms: 0.51 Number of scatterers: 16952 At special positions: 0 Unit cell: (115.482, 115.482, 142.225, 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 120 16.00 O 2888 8.00 N 2844 7.00 C 11100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 2.7 seconds 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 65.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'D' and resid 448 through 457 removed outlier: 3.976A pdb=" N PHE D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 467 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 516 through 522 removed outlier: 4.207A pdb=" N HIS D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 537 removed outlier: 3.740A pdb=" N LEU D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN D 537 " --> pdb=" O ILE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 556 Processing helix chain 'D' and resid 560 through 569 removed outlier: 4.355A pdb=" N VAL D 564 " --> pdb=" O HIS D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 589 Processing helix chain 'D' and resid 592 through 602 removed outlier: 4.150A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG D 601 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER D 602 " --> pdb=" O THR D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 627 Processing helix chain 'D' and resid 629 through 637 removed outlier: 3.575A pdb=" N CYS D 633 " --> pdb=" O TYR D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 691 Processing helix chain 'D' and resid 703 through 740 removed outlier: 3.763A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET D 721 " --> pdb=" O ARG D 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 766 through 783 removed outlier: 3.548A pdb=" N ILE D 770 " --> pdb=" O ASN D 766 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE D 782 " --> pdb=" O PHE D 778 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE D 783 " --> pdb=" O LEU D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 820 removed outlier: 3.753A pdb=" N TYR D 812 " --> pdb=" O GLU D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 828 through 850 removed outlier: 3.694A pdb=" N ALA D 836 " --> pdb=" O TRP D 832 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG D 872 " --> pdb=" O LYS D 868 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER D 873 " --> pdb=" O THR D 869 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 913 removed outlier: 4.276A pdb=" N LEU D 913 " --> pdb=" O PHE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 929 Processing helix chain 'D' and resid 933 through 948 removed outlier: 4.001A pdb=" N ALA D 939 " --> pdb=" O VAL D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 970 removed outlier: 3.965A pdb=" N HIS D 970 " --> pdb=" O ASP D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 988 removed outlier: 4.264A pdb=" N LYS D 974 " --> pdb=" O HIS D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE D1044 " --> pdb=" O LEU D1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D1049 " --> pdb=" O LEU D1045 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG D1050 " --> pdb=" O LYS D1046 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS D1060 " --> pdb=" O PHE D1056 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D1071 " --> pdb=" O LEU D1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 removed outlier: 3.977A pdb=" N PHE A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 516 through 522 removed outlier: 4.207A pdb=" N HIS A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.740A pdb=" N LEU A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'A' and resid 560 through 569 removed outlier: 4.356A pdb=" N VAL A 564 " --> pdb=" O HIS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 592 through 602 removed outlier: 4.150A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 602 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 627 Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.574A pdb=" N CYS A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 703 through 740 removed outlier: 3.764A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 766 through 783 removed outlier: 3.547A pdb=" N ILE A 770 " --> pdb=" O ASN A 766 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 782 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 783 " --> pdb=" O LEU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 820 removed outlier: 3.752A pdb=" N TYR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 828 through 850 removed outlier: 3.695A pdb=" N ALA A 836 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG A 872 " --> pdb=" O LYS A 868 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 913 removed outlier: 4.278A pdb=" N LEU A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 929 Processing helix chain 'A' and resid 933 through 948 removed outlier: 4.003A pdb=" N ALA A 939 " --> pdb=" O VAL A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 970 removed outlier: 3.964A pdb=" N HIS A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 988 removed outlier: 4.264A pdb=" N LYS A 974 " --> pdb=" O HIS A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A1050 " --> pdb=" O LYS A1046 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS A1060 " --> pdb=" O PHE A1056 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 removed outlier: 3.975A pdb=" N PHE B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 516 through 522 removed outlier: 4.208A pdb=" N HIS B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 537 removed outlier: 3.741A pdb=" N LEU B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'B' and resid 560 through 569 removed outlier: 4.355A pdb=" N VAL B 564 " --> pdb=" O HIS B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 602 removed outlier: 4.151A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 602 " --> pdb=" O THR B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 629 through 637 removed outlier: 3.575A pdb=" N CYS B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 691 Processing helix chain 'B' and resid 703 through 740 removed outlier: 3.763A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 721 " --> pdb=" O ARG B 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 766 through 783 removed outlier: 3.546A pdb=" N ILE B 770 " --> pdb=" O ASN B 766 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 782 " --> pdb=" O PHE B 778 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 820 removed outlier: 3.753A pdb=" N TYR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 828 through 850 removed outlier: 3.696A pdb=" N ALA B 836 " --> pdb=" O TRP B 832 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG B 872 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 873 " --> pdb=" O THR B 869 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 913 removed outlier: 4.277A pdb=" N LEU B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 929 Processing helix chain 'B' and resid 933 through 948 removed outlier: 4.002A pdb=" N ALA B 939 " --> pdb=" O VAL B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 970 removed outlier: 3.964A pdb=" N HIS B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 988 removed outlier: 4.265A pdb=" N LYS B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B1049 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B1050 " --> pdb=" O LYS B1046 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B1060 " --> pdb=" O PHE B1056 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 removed outlier: 3.976A pdb=" N PHE C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 467 Processing helix chain 'C' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 516 through 522 removed outlier: 4.207A pdb=" N HIS C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 537 removed outlier: 3.740A pdb=" N LEU C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 556 Processing helix chain 'C' and resid 560 through 569 removed outlier: 4.356A pdb=" N VAL C 564 " --> pdb=" O HIS C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 592 through 602 removed outlier: 4.151A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG C 601 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER C 602 " --> pdb=" O THR C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 627 Processing helix chain 'C' and resid 629 through 637 removed outlier: 3.574A pdb=" N CYS C 633 " --> pdb=" O TYR C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 691 Processing helix chain 'C' and resid 703 through 740 removed outlier: 3.764A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 721 " --> pdb=" O ARG C 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 766 through 783 removed outlier: 3.548A pdb=" N ILE C 770 " --> pdb=" O ASN C 766 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 782 " --> pdb=" O PHE C 778 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 783 " --> pdb=" O LEU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 820 removed outlier: 3.752A pdb=" N TYR C 812 " --> pdb=" O GLU C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 828 through 850 removed outlier: 3.694A pdb=" N ALA C 836 " --> pdb=" O TRP C 832 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG C 872 " --> pdb=" O LYS C 868 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 873 " --> pdb=" O THR C 869 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 913 removed outlier: 4.278A pdb=" N LEU C 913 " --> pdb=" O PHE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 929 Processing helix chain 'C' and resid 933 through 948 removed outlier: 4.001A pdb=" N ALA C 939 " --> pdb=" O VAL C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 970 removed outlier: 3.963A pdb=" N HIS C 970 " --> pdb=" O ASP C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 988 removed outlier: 4.265A pdb=" N LYS C 974 " --> pdb=" O HIS C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR C1049 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C1050 " --> pdb=" O LYS C1046 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C1060 " --> pdb=" O PHE C1056 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C1071 " --> pdb=" O LEU C1067 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2712 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: 4.40 Time building geometry restraints manager: 6.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2661 1.32 - 1.44: 4574 1.44 - 1.57: 9837 1.57 - 1.69: 36 1.69 - 1.82: 196 Bond restraints: 17304 Sorted by residual: bond pdb=" CA VAL C 824 " pdb=" CB VAL C 824 " ideal model delta sigma weight residual 1.540 1.612 -0.072 1.36e-02 5.41e+03 2.82e+01 bond pdb=" CA VAL B 824 " pdb=" CB VAL B 824 " ideal model delta sigma weight residual 1.540 1.612 -0.072 1.36e-02 5.41e+03 2.81e+01 bond pdb=" CA VAL D 824 " pdb=" CB VAL D 824 " ideal model delta sigma weight residual 1.540 1.612 -0.072 1.36e-02 5.41e+03 2.80e+01 bond pdb=" CA VAL A 824 " pdb=" CB VAL A 824 " ideal model delta sigma weight residual 1.540 1.612 -0.071 1.36e-02 5.41e+03 2.76e+01 bond pdb=" CA LEU D 480 " pdb=" C LEU D 480 " ideal model delta sigma weight residual 1.524 1.578 -0.055 1.26e-02 6.30e+03 1.89e+01 ... (remaining 17299 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.37: 352 105.37 - 112.82: 8895 112.82 - 120.27: 7308 120.27 - 127.72: 6733 127.72 - 135.17: 200 Bond angle restraints: 23488 Sorted by residual: angle pdb=" C GLU C 681 " pdb=" N PRO C 682 " pdb=" CA PRO C 682 " ideal model delta sigma weight residual 119.78 129.49 -9.71 1.03e+00 9.43e-01 8.89e+01 angle pdb=" C GLU D 681 " pdb=" N PRO D 682 " pdb=" CA PRO D 682 " ideal model delta sigma weight residual 119.78 129.47 -9.69 1.03e+00 9.43e-01 8.84e+01 angle pdb=" C GLU A 681 " pdb=" N PRO A 682 " pdb=" CA PRO A 682 " ideal model delta sigma weight residual 119.78 129.46 -9.68 1.03e+00 9.43e-01 8.83e+01 angle pdb=" C GLU B 681 " pdb=" N PRO B 682 " pdb=" CA PRO B 682 " ideal model delta sigma weight residual 119.78 129.45 -9.67 1.03e+00 9.43e-01 8.81e+01 angle pdb=" N ASN A 766 " pdb=" CA ASN A 766 " pdb=" CB ASN A 766 " ideal model delta sigma weight residual 112.41 126.89 -14.48 1.55e+00 4.16e-01 8.73e+01 ... (remaining 23483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 9343 22.99 - 45.98: 729 45.98 - 68.97: 152 68.97 - 91.97: 20 91.97 - 114.96: 4 Dihedral angle restraints: 10248 sinusoidal: 3652 harmonic: 6596 Sorted by residual: dihedral pdb=" CA PHE A 612 " pdb=" C PHE A 612 " pdb=" N SER A 613 " pdb=" CA SER A 613 " ideal model delta harmonic sigma weight residual -180.00 -65.04 -114.96 0 5.00e+00 4.00e-02 5.29e+02 dihedral pdb=" CA PHE B 612 " pdb=" C PHE B 612 " pdb=" N SER B 613 " pdb=" CA SER B 613 " ideal model delta harmonic sigma weight residual -180.00 -65.09 -114.91 0 5.00e+00 4.00e-02 5.28e+02 dihedral pdb=" CA PHE C 612 " pdb=" C PHE C 612 " pdb=" N SER C 613 " pdb=" CA SER C 613 " ideal model delta harmonic sigma weight residual -180.00 -65.12 -114.88 0 5.00e+00 4.00e-02 5.28e+02 ... (remaining 10245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2146 0.077 - 0.155: 580 0.155 - 0.232: 58 0.232 - 0.309: 16 0.309 - 0.386: 8 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CA VAL A 824 " pdb=" N VAL A 824 " pdb=" C VAL A 824 " pdb=" CB VAL A 824 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA VAL C 824 " pdb=" N VAL C 824 " pdb=" C VAL C 824 " pdb=" CB VAL C 824 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA VAL D 824 " pdb=" N VAL D 824 " pdb=" C VAL D 824 " pdb=" CB VAL D 824 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 2805 not shown) Planarity restraints: 2888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D1047 " -0.038 2.00e-02 2.50e+03 7.60e-02 5.77e+01 pdb=" CD GLN D1047 " 0.131 2.00e-02 2.50e+03 pdb=" OE1 GLN D1047 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN D1047 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C1047 " -0.038 2.00e-02 2.50e+03 7.58e-02 5.75e+01 pdb=" CD GLN C1047 " 0.131 2.00e-02 2.50e+03 pdb=" OE1 GLN C1047 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN C1047 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B1047 " 0.038 2.00e-02 2.50e+03 7.55e-02 5.71e+01 pdb=" CD GLN B1047 " -0.131 2.00e-02 2.50e+03 pdb=" OE1 GLN B1047 " 0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN B1047 " 0.044 2.00e-02 2.50e+03 ... (remaining 2885 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 628 2.67 - 3.23: 18247 3.23 - 3.79: 25629 3.79 - 4.34: 31485 4.34 - 4.90: 48026 Nonbonded interactions: 124015 Sorted by model distance: nonbonded pdb=" O MET A1072 " pdb=" NH2 ARG B 458 " model vdw 2.113 2.520 nonbonded pdb=" O HIS C 970 " pdb=" ND1 HIS C 970 " model vdw 2.123 2.520 nonbonded pdb=" O HIS D 970 " pdb=" ND1 HIS D 970 " model vdw 2.123 2.520 nonbonded pdb=" O HIS B 970 " pdb=" ND1 HIS B 970 " model vdw 2.123 2.520 nonbonded pdb=" O HIS A 970 " pdb=" ND1 HIS A 970 " model vdw 2.123 2.520 ... (remaining 124010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.490 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 40.860 Find NCS groups from input model: 0.990 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.009 0.072 17304 Z= 0.573 Angle : 1.852 14.481 23488 Z= 1.228 Chirality : 0.070 0.386 2808 Planarity : 0.006 0.076 2888 Dihedral : 17.684 114.956 5952 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 1.64 % Allowed : 10.18 % Favored : 88.18 % Rotamer: Outliers : 4.64 % Allowed : 24.04 % Favored : 71.33 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.68 % Twisted Proline : 5.56 % Twisted General : 3.96 % 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: -3.58 (0.15), residues: 2200 helix: -1.89 (0.11), residues: 1412 sheet: None (None), residues: 0 loop : -3.09 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 605 HIS 0.055 0.005 HIS A 481 PHE 0.041 0.004 PHE B 877 TYR 0.041 0.004 TYR B 842 ARG 0.011 0.001 ARG C 604 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 443 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 819 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8948 (m) REVERT: D 844 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8205 (tmm) REVERT: D 955 LEU cc_start: 0.9112 (tt) cc_final: 0.8700 (tt) REVERT: D 959 LEU cc_start: 0.9194 (mp) cc_final: 0.8600 (mp) REVERT: A 819 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8968 (m) REVERT: A 844 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8222 (tmm) REVERT: A 955 LEU cc_start: 0.9055 (tt) cc_final: 0.8643 (tt) REVERT: A 959 LEU cc_start: 0.9172 (mp) cc_final: 0.8574 (mp) REVERT: A 1050 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7698 (mtt-85) REVERT: B 819 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8972 (m) REVERT: B 955 LEU cc_start: 0.9072 (tt) cc_final: 0.8641 (tt) REVERT: B 959 LEU cc_start: 0.9196 (mp) cc_final: 0.8615 (mp) REVERT: B 1050 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7697 (mtt-85) REVERT: C 819 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8960 (m) REVERT: C 844 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8181 (tmm) REVERT: C 959 LEU cc_start: 0.9197 (mp) cc_final: 0.8682 (mp) REVERT: C 1050 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7700 (mtt-85) outliers start: 77 outliers final: 20 residues processed: 492 average time/residue: 0.2901 time to fit residues: 208.8021 Evaluate side-chains 297 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 267 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.5980 chunk 169 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 175 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 570 HIS ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 766 ASN ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN A 570 HIS ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 ASN ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17304 Z= 0.272 Angle : 1.004 12.863 23488 Z= 0.521 Chirality : 0.048 0.205 2808 Planarity : 0.004 0.031 2888 Dihedral : 8.032 46.966 2356 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 1.09 % Allowed : 7.82 % Favored : 91.09 % Rotamer: Outliers : 0.24 % Allowed : 4.94 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 4.10 % Twisted Proline : 0.00 % Twisted General : 0.74 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2200 helix: -0.67 (0.13), residues: 1404 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 605 HIS 0.007 0.002 HIS A 487 PHE 0.042 0.002 PHE D 877 TYR 0.026 0.002 TYR C 842 ARG 0.010 0.001 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 371 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 486 LEU cc_start: 0.9388 (mp) cc_final: 0.9115 (tp) REVERT: D 634 MET cc_start: 0.9009 (tmm) cc_final: 0.8712 (tmm) REVERT: D 706 TYR cc_start: 0.8777 (m-80) cc_final: 0.8468 (m-10) REVERT: D 727 CYS cc_start: 0.8786 (t) cc_final: 0.8556 (t) REVERT: D 844 MET cc_start: 0.8471 (ttm) cc_final: 0.8174 (tpt) REVERT: D 959 LEU cc_start: 0.9071 (mp) cc_final: 0.8808 (mt) REVERT: A 486 LEU cc_start: 0.9390 (mp) cc_final: 0.9115 (tp) REVERT: A 634 MET cc_start: 0.9007 (tmm) cc_final: 0.8712 (tmm) REVERT: A 697 LEU cc_start: 0.8483 (mt) cc_final: 0.8248 (mt) REVERT: A 706 TYR cc_start: 0.8790 (m-80) cc_final: 0.8476 (m-10) REVERT: A 727 CYS cc_start: 0.8767 (t) cc_final: 0.8545 (t) REVERT: A 844 MET cc_start: 0.8453 (ttm) cc_final: 0.8133 (tpt) REVERT: A 959 LEU cc_start: 0.9091 (mp) cc_final: 0.8810 (mt) REVERT: B 486 LEU cc_start: 0.9389 (mp) cc_final: 0.9122 (tp) REVERT: B 634 MET cc_start: 0.8987 (tmm) cc_final: 0.8699 (tmm) REVERT: B 697 LEU cc_start: 0.8486 (mt) cc_final: 0.8241 (mt) REVERT: B 706 TYR cc_start: 0.8797 (m-80) cc_final: 0.8489 (m-10) REVERT: B 727 CYS cc_start: 0.8792 (t) cc_final: 0.8556 (t) REVERT: B 844 MET cc_start: 0.8211 (tmm) cc_final: 0.7706 (tpt) REVERT: B 959 LEU cc_start: 0.9090 (mp) cc_final: 0.8813 (mt) REVERT: C 486 LEU cc_start: 0.9387 (mp) cc_final: 0.9114 (tp) REVERT: C 634 MET cc_start: 0.8988 (tmm) cc_final: 0.8692 (tmm) REVERT: C 697 LEU cc_start: 0.8496 (mt) cc_final: 0.8277 (mt) REVERT: C 706 TYR cc_start: 0.8798 (m-80) cc_final: 0.8487 (m-10) REVERT: C 711 TRP cc_start: 0.8427 (m100) cc_final: 0.8159 (m100) REVERT: C 727 CYS cc_start: 0.8793 (t) cc_final: 0.8557 (t) REVERT: C 844 MET cc_start: 0.8472 (ttm) cc_final: 0.8167 (tpt) REVERT: C 1042 MET cc_start: 0.8356 (ppp) cc_final: 0.8154 (ppp) outliers start: 4 outliers final: 0 residues processed: 371 average time/residue: 0.2474 time to fit residues: 143.1165 Evaluate side-chains 227 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 220 optimal weight: 0.0980 chunk 181 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 163 optimal weight: 40.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 829 HIS ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 HIS ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 HIS ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17304 Z= 0.285 Angle : 0.923 11.509 23488 Z= 0.488 Chirality : 0.046 0.193 2808 Planarity : 0.005 0.037 2888 Dihedral : 6.988 31.039 2356 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 1.09 % Allowed : 8.86 % Favored : 90.05 % Rotamer: Outliers : 0.42 % Allowed : 5.54 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -2.05 (0.17), residues: 2200 helix: -0.40 (0.13), residues: 1404 sheet: None (None), residues: 0 loop : -3.12 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 605 HIS 0.007 0.001 HIS C 512 PHE 0.045 0.002 PHE A 716 TYR 0.023 0.002 TYR A 842 ARG 0.007 0.001 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 298 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 502 LEU cc_start: 0.9008 (mm) cc_final: 0.8802 (pp) REVERT: D 697 LEU cc_start: 0.8601 (mt) cc_final: 0.8189 (mt) REVERT: D 706 TYR cc_start: 0.8800 (m-80) cc_final: 0.8483 (m-10) REVERT: D 844 MET cc_start: 0.8575 (ttm) cc_final: 0.8087 (tpt) REVERT: D 1056 PHE cc_start: 0.9166 (t80) cc_final: 0.8761 (t80) REVERT: A 502 LEU cc_start: 0.9001 (mm) cc_final: 0.8798 (pp) REVERT: A 697 LEU cc_start: 0.8566 (mt) cc_final: 0.8166 (mt) REVERT: A 706 TYR cc_start: 0.8805 (m-80) cc_final: 0.8485 (m-10) REVERT: A 844 MET cc_start: 0.8676 (ttm) cc_final: 0.8128 (tpt) REVERT: A 1056 PHE cc_start: 0.9164 (t80) cc_final: 0.8746 (t80) REVERT: A 1068 ILE cc_start: 0.9262 (mm) cc_final: 0.9051 (mm) REVERT: B 479 ASP cc_start: 0.7970 (p0) cc_final: 0.7341 (p0) REVERT: B 502 LEU cc_start: 0.9013 (mm) cc_final: 0.8809 (pp) REVERT: B 697 LEU cc_start: 0.8558 (mt) cc_final: 0.8154 (mt) REVERT: B 706 TYR cc_start: 0.8813 (m-80) cc_final: 0.8491 (m-10) REVERT: B 844 MET cc_start: 0.8593 (ttp) cc_final: 0.8037 (tpt) REVERT: B 915 ASP cc_start: 0.7141 (p0) cc_final: 0.6832 (p0) REVERT: B 1056 PHE cc_start: 0.9164 (t80) cc_final: 0.8761 (t80) REVERT: C 479 ASP cc_start: 0.7987 (p0) cc_final: 0.7337 (p0) REVERT: C 502 LEU cc_start: 0.9032 (mm) cc_final: 0.8830 (pp) REVERT: C 697 LEU cc_start: 0.8507 (mt) cc_final: 0.8049 (mt) REVERT: C 706 TYR cc_start: 0.8803 (m-80) cc_final: 0.8538 (m-80) REVERT: C 844 MET cc_start: 0.8624 (ttm) cc_final: 0.8073 (tpt) REVERT: C 915 ASP cc_start: 0.7184 (p0) cc_final: 0.6676 (p0) REVERT: C 1056 PHE cc_start: 0.9155 (t80) cc_final: 0.8753 (t80) outliers start: 7 outliers final: 0 residues processed: 305 average time/residue: 0.2487 time to fit residues: 119.2080 Evaluate side-chains 215 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 193 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17304 Z= 0.207 Angle : 0.868 11.405 23488 Z= 0.449 Chirality : 0.044 0.181 2808 Planarity : 0.005 0.050 2888 Dihedral : 6.285 32.337 2356 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.68 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.86 (0.17), residues: 2200 helix: -0.22 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -3.17 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 809 HIS 0.007 0.001 HIS B 512 PHE 0.039 0.002 PHE C 877 TYR 0.016 0.001 TYR A 842 ARG 0.003 0.000 ARG C 919 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 697 LEU cc_start: 0.8540 (mt) cc_final: 0.8241 (mt) REVERT: D 706 TYR cc_start: 0.8814 (m-80) cc_final: 0.8469 (m-10) REVERT: D 844 MET cc_start: 0.8725 (ttm) cc_final: 0.8263 (tpt) REVERT: D 877 PHE cc_start: 0.8366 (p90) cc_final: 0.8065 (p90) REVERT: D 1056 PHE cc_start: 0.9081 (t80) cc_final: 0.8617 (t80) REVERT: D 1068 ILE cc_start: 0.9038 (mm) cc_final: 0.8780 (mm) REVERT: A 697 LEU cc_start: 0.8504 (mt) cc_final: 0.8282 (mt) REVERT: A 706 TYR cc_start: 0.8819 (m-80) cc_final: 0.8475 (m-10) REVERT: A 844 MET cc_start: 0.8753 (ttm) cc_final: 0.8239 (tpt) REVERT: A 861 VAL cc_start: 0.9226 (m) cc_final: 0.8997 (p) REVERT: A 1056 PHE cc_start: 0.9139 (t80) cc_final: 0.8664 (t80) REVERT: B 697 LEU cc_start: 0.8495 (mt) cc_final: 0.8210 (mt) REVERT: B 706 TYR cc_start: 0.8824 (m-80) cc_final: 0.8481 (m-10) REVERT: B 844 MET cc_start: 0.8742 (ttp) cc_final: 0.8302 (tpt) REVERT: B 861 VAL cc_start: 0.9224 (m) cc_final: 0.8996 (p) REVERT: B 1056 PHE cc_start: 0.9143 (t80) cc_final: 0.8670 (t80) REVERT: B 1068 ILE cc_start: 0.9080 (mm) cc_final: 0.8875 (mm) REVERT: C 697 LEU cc_start: 0.8496 (mt) cc_final: 0.8058 (mt) REVERT: C 706 TYR cc_start: 0.8820 (m-80) cc_final: 0.8489 (m-10) REVERT: C 844 MET cc_start: 0.8702 (ttm) cc_final: 0.8285 (tpt) REVERT: C 861 VAL cc_start: 0.9229 (m) cc_final: 0.9001 (p) REVERT: C 877 PHE cc_start: 0.8395 (p90) cc_final: 0.8067 (p90) REVERT: C 1056 PHE cc_start: 0.9090 (t80) cc_final: 0.8637 (t80) REVERT: C 1068 ILE cc_start: 0.9043 (mm) cc_final: 0.8716 (mm) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2472 time to fit residues: 122.3407 Evaluate side-chains 243 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 10.0000 chunk 122 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 89 optimal weight: 0.0070 chunk 184 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 HIS ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.7047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17304 Z= 0.207 Angle : 0.871 11.207 23488 Z= 0.446 Chirality : 0.044 0.195 2808 Planarity : 0.005 0.052 2888 Dihedral : 5.908 32.403 2356 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.23 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.82 (0.17), residues: 2200 helix: -0.25 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -3.03 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 711 HIS 0.008 0.001 HIS D 933 PHE 0.051 0.001 PHE B 877 TYR 0.016 0.001 TYR C 840 ARG 0.003 0.000 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 697 LEU cc_start: 0.8450 (mt) cc_final: 0.8205 (mt) REVERT: D 706 TYR cc_start: 0.8816 (m-80) cc_final: 0.8520 (m-10) REVERT: D 711 TRP cc_start: 0.8394 (m100) cc_final: 0.8189 (m100) REVERT: D 844 MET cc_start: 0.8698 (ttm) cc_final: 0.8297 (tpt) REVERT: D 880 LEU cc_start: 0.9587 (tt) cc_final: 0.9360 (pp) REVERT: D 913 LEU cc_start: 0.8557 (tp) cc_final: 0.8293 (tp) REVERT: D 1056 PHE cc_start: 0.9255 (t80) cc_final: 0.8899 (t80) REVERT: A 697 LEU cc_start: 0.8488 (mt) cc_final: 0.8061 (mt) REVERT: A 704 LYS cc_start: 0.8692 (mttt) cc_final: 0.8386 (mttt) REVERT: A 706 TYR cc_start: 0.8788 (m-80) cc_final: 0.8566 (m-10) REVERT: A 711 TRP cc_start: 0.8383 (m100) cc_final: 0.8182 (m100) REVERT: A 817 ILE cc_start: 0.9232 (tp) cc_final: 0.9027 (pt) REVERT: A 844 MET cc_start: 0.8715 (ttm) cc_final: 0.8244 (tpt) REVERT: A 877 PHE cc_start: 0.8645 (p90) cc_final: 0.8389 (p90) REVERT: A 1056 PHE cc_start: 0.9229 (t80) cc_final: 0.8887 (t80) REVERT: B 697 LEU cc_start: 0.8484 (mt) cc_final: 0.7989 (mt) REVERT: B 704 LYS cc_start: 0.8612 (mttt) cc_final: 0.8326 (mttt) REVERT: B 706 TYR cc_start: 0.8787 (m-80) cc_final: 0.8504 (m-10) REVERT: B 711 TRP cc_start: 0.8430 (m100) cc_final: 0.8199 (m100) REVERT: B 720 MET cc_start: 0.8162 (mpp) cc_final: 0.7923 (mpp) REVERT: B 844 MET cc_start: 0.8707 (ttp) cc_final: 0.8366 (tpt) REVERT: B 877 PHE cc_start: 0.8596 (p90) cc_final: 0.8162 (p90) REVERT: B 1056 PHE cc_start: 0.9227 (t80) cc_final: 0.8882 (t80) REVERT: B 1068 ILE cc_start: 0.8962 (mm) cc_final: 0.8750 (mm) REVERT: C 697 LEU cc_start: 0.8459 (mt) cc_final: 0.7980 (mt) REVERT: C 704 LYS cc_start: 0.8552 (mttt) cc_final: 0.8284 (mttt) REVERT: C 706 TYR cc_start: 0.8800 (m-80) cc_final: 0.8528 (m-80) REVERT: C 844 MET cc_start: 0.8708 (ttm) cc_final: 0.8279 (tpt) REVERT: C 877 PHE cc_start: 0.8527 (p90) cc_final: 0.8168 (p90) REVERT: C 913 LEU cc_start: 0.8591 (tp) cc_final: 0.8315 (tp) REVERT: C 1056 PHE cc_start: 0.9241 (t80) cc_final: 0.8895 (t80) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2570 time to fit residues: 123.2458 Evaluate side-chains 235 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17304 Z= 0.271 Angle : 0.882 10.639 23488 Z= 0.461 Chirality : 0.044 0.182 2808 Planarity : 0.005 0.050 2888 Dihedral : 6.153 34.257 2356 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.36 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.79 (0.17), residues: 2200 helix: -0.25 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 711 HIS 0.011 0.002 HIS A 933 PHE 0.043 0.002 PHE B 877 TYR 0.047 0.002 TYR D 842 ARG 0.004 0.000 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 697 LEU cc_start: 0.8552 (mt) cc_final: 0.8275 (mt) REVERT: D 706 TYR cc_start: 0.8794 (m-80) cc_final: 0.8445 (m-10) REVERT: D 840 TYR cc_start: 0.8888 (t80) cc_final: 0.8512 (t80) REVERT: D 844 MET cc_start: 0.8690 (ttm) cc_final: 0.8461 (mtp) REVERT: D 877 PHE cc_start: 0.8577 (p90) cc_final: 0.8224 (p90) REVERT: D 1056 PHE cc_start: 0.9251 (t80) cc_final: 0.8948 (t80) REVERT: D 1072 MET cc_start: 0.7921 (mtm) cc_final: 0.7711 (mtt) REVERT: A 697 LEU cc_start: 0.8589 (mt) cc_final: 0.8210 (mt) REVERT: A 706 TYR cc_start: 0.8803 (m-80) cc_final: 0.8453 (m-10) REVERT: A 720 MET cc_start: 0.8264 (mpp) cc_final: 0.7922 (mpp) REVERT: A 844 MET cc_start: 0.8682 (ttm) cc_final: 0.8360 (tpt) REVERT: B 697 LEU cc_start: 0.8561 (mt) cc_final: 0.8257 (mt) REVERT: B 706 TYR cc_start: 0.8835 (m-80) cc_final: 0.8475 (m-10) REVERT: B 720 MET cc_start: 0.8265 (mpp) cc_final: 0.7940 (mpp) REVERT: B 844 MET cc_start: 0.8645 (ttp) cc_final: 0.8372 (tpt) REVERT: B 877 PHE cc_start: 0.8413 (p90) cc_final: 0.8047 (p90) REVERT: B 1056 PHE cc_start: 0.9284 (t80) cc_final: 0.8947 (t80) REVERT: C 697 LEU cc_start: 0.8539 (mt) cc_final: 0.7951 (mt) REVERT: C 704 LYS cc_start: 0.8606 (mttt) cc_final: 0.8401 (mttt) REVERT: C 706 TYR cc_start: 0.8829 (m-80) cc_final: 0.8449 (m-10) REVERT: C 844 MET cc_start: 0.8626 (ttm) cc_final: 0.8312 (tpt) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2563 time to fit residues: 112.4981 Evaluate side-chains 225 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.7730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17304 Z= 0.208 Angle : 0.853 10.816 23488 Z= 0.436 Chirality : 0.043 0.185 2808 Planarity : 0.005 0.050 2888 Dihedral : 5.794 32.638 2356 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.64 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.69 (0.17), residues: 2200 helix: -0.12 (0.13), residues: 1404 sheet: None (None), residues: 0 loop : -2.96 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 711 HIS 0.007 0.001 HIS A 933 PHE 0.040 0.001 PHE B 877 TYR 0.034 0.002 TYR A 842 ARG 0.002 0.000 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 642 MET cc_start: 0.6619 (pmm) cc_final: 0.6377 (pmm) REVERT: D 697 LEU cc_start: 0.8522 (mt) cc_final: 0.8220 (mt) REVERT: D 706 TYR cc_start: 0.8745 (m-80) cc_final: 0.8422 (m-10) REVERT: D 840 TYR cc_start: 0.8883 (t80) cc_final: 0.8512 (t80) REVERT: D 844 MET cc_start: 0.8666 (ttm) cc_final: 0.8287 (mmm) REVERT: D 877 PHE cc_start: 0.8521 (p90) cc_final: 0.8116 (p90) REVERT: D 1056 PHE cc_start: 0.9169 (t80) cc_final: 0.8855 (t80) REVERT: A 642 MET cc_start: 0.6616 (pmm) cc_final: 0.6377 (pmm) REVERT: A 706 TYR cc_start: 0.8701 (m-80) cc_final: 0.8413 (m-10) REVERT: A 844 MET cc_start: 0.8648 (ttm) cc_final: 0.8288 (mmm) REVERT: A 877 PHE cc_start: 0.8611 (p90) cc_final: 0.8276 (p90) REVERT: A 1056 PHE cc_start: 0.9215 (t80) cc_final: 0.8870 (t80) REVERT: B 503 LYS cc_start: 0.9408 (ttpt) cc_final: 0.9187 (ptmt) REVERT: B 545 ASP cc_start: 0.6635 (p0) cc_final: 0.6096 (p0) REVERT: B 642 MET cc_start: 0.6602 (pmm) cc_final: 0.6374 (pmm) REVERT: B 697 LEU cc_start: 0.8541 (mt) cc_final: 0.8034 (mt) REVERT: B 706 TYR cc_start: 0.8750 (m-80) cc_final: 0.8445 (m-10) REVERT: B 720 MET cc_start: 0.8268 (mpp) cc_final: 0.7847 (mpp) REVERT: B 844 MET cc_start: 0.8623 (ttp) cc_final: 0.8339 (tpt) REVERT: B 877 PHE cc_start: 0.8419 (p90) cc_final: 0.8172 (p90) REVERT: B 1056 PHE cc_start: 0.9226 (t80) cc_final: 0.8874 (t80) REVERT: C 697 LEU cc_start: 0.8523 (mt) cc_final: 0.8017 (mt) REVERT: C 706 TYR cc_start: 0.8795 (m-80) cc_final: 0.8461 (m-10) REVERT: C 840 TYR cc_start: 0.8895 (t80) cc_final: 0.8556 (t80) REVERT: C 844 MET cc_start: 0.8607 (ttm) cc_final: 0.8219 (mmm) REVERT: C 877 PHE cc_start: 0.8464 (p90) cc_final: 0.8140 (p90) REVERT: C 913 LEU cc_start: 0.8706 (tp) cc_final: 0.8477 (tp) REVERT: C 1056 PHE cc_start: 0.9210 (t80) cc_final: 0.8879 (t80) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2646 time to fit residues: 123.3601 Evaluate side-chains 231 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 907 GLN ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.7916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17304 Z= 0.248 Angle : 0.870 10.632 23488 Z= 0.452 Chirality : 0.044 0.177 2808 Planarity : 0.005 0.053 2888 Dihedral : 5.871 33.401 2356 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.00 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.72 (0.17), residues: 2200 helix: -0.14 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -3.02 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 515 HIS 0.007 0.001 HIS A 933 PHE 0.037 0.002 PHE B 877 TYR 0.034 0.002 TYR C 842 ARG 0.004 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 545 ASP cc_start: 0.6789 (p0) cc_final: 0.6518 (p0) REVERT: D 642 MET cc_start: 0.6588 (pmm) cc_final: 0.6260 (pmm) REVERT: D 697 LEU cc_start: 0.8457 (mt) cc_final: 0.7860 (mt) REVERT: D 706 TYR cc_start: 0.8769 (m-80) cc_final: 0.8427 (m-10) REVERT: D 711 TRP cc_start: 0.8606 (m100) cc_final: 0.8321 (m100) REVERT: D 840 TYR cc_start: 0.8882 (t80) cc_final: 0.8404 (t80) REVERT: D 844 MET cc_start: 0.8618 (ttm) cc_final: 0.8315 (mmm) REVERT: D 1068 ILE cc_start: 0.9402 (mt) cc_final: 0.8893 (mt) REVERT: D 1072 MET cc_start: 0.8279 (mmt) cc_final: 0.7656 (mmm) REVERT: A 642 MET cc_start: 0.6595 (pmm) cc_final: 0.6267 (pmm) REVERT: A 706 TYR cc_start: 0.8821 (m-80) cc_final: 0.8471 (m-10) REVERT: A 711 TRP cc_start: 0.8557 (m100) cc_final: 0.8271 (m100) REVERT: A 720 MET cc_start: 0.8319 (mpp) cc_final: 0.7882 (mpp) REVERT: A 840 TYR cc_start: 0.8805 (t80) cc_final: 0.8333 (t80) REVERT: A 844 MET cc_start: 0.8547 (ttm) cc_final: 0.8246 (mmm) REVERT: A 877 PHE cc_start: 0.8572 (p90) cc_final: 0.8199 (p90) REVERT: A 1068 ILE cc_start: 0.9151 (mm) cc_final: 0.8912 (mm) REVERT: B 642 MET cc_start: 0.6583 (pmm) cc_final: 0.6262 (pmm) REVERT: B 706 TYR cc_start: 0.8785 (m-80) cc_final: 0.8412 (m-10) REVERT: B 711 TRP cc_start: 0.8583 (m100) cc_final: 0.8286 (m100) REVERT: B 840 TYR cc_start: 0.8953 (t80) cc_final: 0.8111 (t80) REVERT: B 877 PHE cc_start: 0.8368 (p90) cc_final: 0.8021 (p90) REVERT: B 950 ILE cc_start: 0.8887 (pt) cc_final: 0.8466 (tt) REVERT: C 642 MET cc_start: 0.6574 (pmm) cc_final: 0.6257 (pmm) REVERT: C 697 LEU cc_start: 0.8420 (mt) cc_final: 0.7753 (mt) REVERT: C 706 TYR cc_start: 0.8777 (m-80) cc_final: 0.8439 (m-10) REVERT: C 720 MET cc_start: 0.8218 (mpp) cc_final: 0.7972 (mpp) REVERT: C 840 TYR cc_start: 0.8904 (t80) cc_final: 0.8426 (t80) REVERT: C 844 MET cc_start: 0.8522 (ttm) cc_final: 0.8256 (mmm) REVERT: C 913 LEU cc_start: 0.8757 (tp) cc_final: 0.8495 (tp) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2576 time to fit residues: 109.1454 Evaluate side-chains 217 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 121 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 GLN C 954 ASN ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.8082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17304 Z= 0.216 Angle : 0.857 10.858 23488 Z= 0.440 Chirality : 0.043 0.181 2808 Planarity : 0.005 0.054 2888 Dihedral : 5.645 32.429 2356 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.95 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.69 (0.17), residues: 2200 helix: -0.10 (0.13), residues: 1404 sheet: None (None), residues: 0 loop : -3.02 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 605 HIS 0.006 0.001 HIS D 512 PHE 0.044 0.002 PHE C 877 TYR 0.029 0.002 TYR D 842 ARG 0.005 0.000 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 642 MET cc_start: 0.6659 (pmm) cc_final: 0.6379 (pmm) REVERT: D 706 TYR cc_start: 0.8757 (m-80) cc_final: 0.8433 (m-10) REVERT: D 711 TRP cc_start: 0.8570 (m100) cc_final: 0.8278 (m100) REVERT: D 840 TYR cc_start: 0.8801 (t80) cc_final: 0.8527 (t80) REVERT: D 1068 ILE cc_start: 0.9374 (mt) cc_final: 0.8866 (mt) REVERT: D 1072 MET cc_start: 0.8330 (mmt) cc_final: 0.7941 (mmm) REVERT: A 642 MET cc_start: 0.6663 (pmm) cc_final: 0.6391 (pmm) REVERT: A 706 TYR cc_start: 0.8811 (m-80) cc_final: 0.8450 (m-10) REVERT: A 711 TRP cc_start: 0.8574 (m100) cc_final: 0.8278 (m100) REVERT: A 720 MET cc_start: 0.8302 (mpp) cc_final: 0.7874 (mpp) REVERT: A 840 TYR cc_start: 0.8799 (t80) cc_final: 0.8347 (t80) REVERT: A 844 MET cc_start: 0.8605 (ttm) cc_final: 0.8316 (mmm) REVERT: A 877 PHE cc_start: 0.8593 (p90) cc_final: 0.8229 (p90) REVERT: A 1068 ILE cc_start: 0.9130 (mm) cc_final: 0.8911 (mm) REVERT: B 642 MET cc_start: 0.6658 (pmm) cc_final: 0.6382 (pmm) REVERT: B 706 TYR cc_start: 0.8897 (m-80) cc_final: 0.8530 (m-10) REVERT: B 711 TRP cc_start: 0.8576 (m100) cc_final: 0.8276 (m100) REVERT: B 840 TYR cc_start: 0.8873 (t80) cc_final: 0.8600 (t80) REVERT: B 877 PHE cc_start: 0.8357 (p90) cc_final: 0.8134 (p90) REVERT: B 950 ILE cc_start: 0.8822 (pt) cc_final: 0.8549 (tt) REVERT: B 1068 ILE cc_start: 0.9166 (mt) cc_final: 0.8934 (mm) REVERT: C 547 ASP cc_start: 0.8349 (p0) cc_final: 0.8122 (p0) REVERT: C 642 MET cc_start: 0.6645 (pmm) cc_final: 0.6378 (pmm) REVERT: C 706 TYR cc_start: 0.8767 (m-80) cc_final: 0.8434 (m-10) REVERT: C 840 TYR cc_start: 0.8902 (t80) cc_final: 0.8370 (t80) REVERT: C 844 MET cc_start: 0.8504 (ttm) cc_final: 0.8242 (mmm) REVERT: C 913 LEU cc_start: 0.8666 (tp) cc_final: 0.8352 (tp) REVERT: C 915 ASP cc_start: 0.7113 (p0) cc_final: 0.6850 (p0) REVERT: C 1068 ILE cc_start: 0.9402 (mt) cc_final: 0.9064 (mm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2521 time to fit residues: 106.0294 Evaluate side-chains 219 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 129 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 147 optimal weight: 0.0670 chunk 223 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 overall best weight: 1.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 HIS ** 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: 0.8213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17304 Z= 0.215 Angle : 0.870 10.842 23488 Z= 0.446 Chirality : 0.043 0.179 2808 Planarity : 0.005 0.055 2888 Dihedral : 5.539 31.839 2356 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.55 % Favored : 89.73 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.73 (0.17), residues: 2200 helix: -0.18 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -2.94 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 605 HIS 0.006 0.001 HIS D 512 PHE 0.040 0.002 PHE C 877 TYR 0.028 0.002 TYR C 842 ARG 0.005 0.000 ARG A 975 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 642 MET cc_start: 0.6663 (pmm) cc_final: 0.6384 (pmm) REVERT: D 706 TYR cc_start: 0.8786 (m-80) cc_final: 0.8418 (m-10) REVERT: D 711 TRP cc_start: 0.8531 (m100) cc_final: 0.8271 (m100) REVERT: D 840 TYR cc_start: 0.8771 (t80) cc_final: 0.8514 (t80) REVERT: A 642 MET cc_start: 0.6643 (pmm) cc_final: 0.6378 (pmm) REVERT: A 706 TYR cc_start: 0.8886 (m-80) cc_final: 0.8506 (m-10) REVERT: A 711 TRP cc_start: 0.8582 (m100) cc_final: 0.8310 (m100) REVERT: A 720 MET cc_start: 0.8298 (mpp) cc_final: 0.7831 (mpp) REVERT: A 840 TYR cc_start: 0.8780 (t80) cc_final: 0.8283 (t80) REVERT: A 844 MET cc_start: 0.8565 (ttm) cc_final: 0.8267 (mmm) REVERT: B 503 LYS cc_start: 0.9441 (ttpt) cc_final: 0.9206 (ptmt) REVERT: B 642 MET cc_start: 0.6634 (pmm) cc_final: 0.6365 (pmm) REVERT: B 706 TYR cc_start: 0.8815 (m-80) cc_final: 0.8455 (m-10) REVERT: B 711 TRP cc_start: 0.8592 (m100) cc_final: 0.8316 (m100) REVERT: B 720 MET cc_start: 0.8220 (mpp) cc_final: 0.7789 (mpp) REVERT: B 844 MET cc_start: 0.8588 (mmm) cc_final: 0.8377 (mmt) REVERT: B 913 LEU cc_start: 0.8743 (tp) cc_final: 0.8448 (tp) REVERT: B 950 ILE cc_start: 0.8846 (pt) cc_final: 0.8595 (tp) REVERT: B 1068 ILE cc_start: 0.9243 (mt) cc_final: 0.9008 (mm) REVERT: C 642 MET cc_start: 0.6632 (pmm) cc_final: 0.6373 (pmm) REVERT: C 706 TYR cc_start: 0.8777 (m-80) cc_final: 0.8454 (m-10) REVERT: C 720 MET cc_start: 0.8193 (mpp) cc_final: 0.7833 (mpp) REVERT: C 840 TYR cc_start: 0.8883 (t80) cc_final: 0.8315 (t80) REVERT: C 844 MET cc_start: 0.8515 (ttm) cc_final: 0.8264 (mmm) REVERT: C 913 LEU cc_start: 0.8780 (tp) cc_final: 0.8456 (tp) REVERT: C 1068 ILE cc_start: 0.9417 (mt) cc_final: 0.9154 (mm) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2434 time to fit residues: 103.2702 Evaluate side-chains 215 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 163 optimal weight: 50.0000 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** 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 = 0.2937 r_free = 0.2937 target = 0.043346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.034045 restraints weight = 121507.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.035056 restraints weight = 87991.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.035872 restraints weight = 67538.449| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.8392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17304 Z= 0.217 Angle : 0.863 10.850 23488 Z= 0.443 Chirality : 0.043 0.231 2808 Planarity : 0.005 0.055 2888 Dihedral : 5.524 31.775 2356 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.86 % Allowed : 9.36 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.66 (0.17), residues: 2200 helix: -0.14 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -2.88 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 605 HIS 0.006 0.001 HIS D 512 PHE 0.037 0.002 PHE C 877 TYR 0.028 0.002 TYR C 842 ARG 0.005 0.000 ARG A 458 =============================================================================== Job complete usr+sys time: 3164.66 seconds wall clock time: 58 minutes 24.08 seconds (3504.08 seconds total)