Starting phenix.real_space_refine on Sun Mar 17 05:00:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/03_2024/7rz8_24754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/03_2024/7rz8_24754.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/03_2024/7rz8_24754_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/03_2024/7rz8_24754_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/03_2024/7rz8_24754_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/03_2024/7rz8_24754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/03_2024/7rz8_24754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/03_2024/7rz8_24754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/03_2024/7rz8_24754_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 106 5.16 5 C 10960 2.51 5 N 2600 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "B GLU 821": "OE1" <-> "OE2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 819": "NH1" <-> "NH2" Residue "D GLU 821": "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: 16722 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4762 Classifications: {'peptide': 609} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 591} Chain breaks: 3 Chain: "B" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3216 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 399} Chain breaks: 1 Chain: "C" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4762 Classifications: {'peptide': 609} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 591} Chain breaks: 3 Chain: "D" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3216 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 399} Chain breaks: 1 Chain: "A" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Unusual residues: {'PCW': 7, 'QUS': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'PCW': 4, 'QUS': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Unusual residues: {'PCW': 7, 'QUS': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'PCW': 4, 'QUS': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 8.86, per 1000 atoms: 0.53 Number of scatterers: 16722 At special positions: 0 Unit cell: (118.659, 131.487, 132.556, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 14 15.00 O 3042 8.00 N 2600 7.00 C 10960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.05 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.05 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 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: 6.05 Conformation dependent library (CDL) restraints added in 2.8 seconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 14 sheets defined 51.6% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.524A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.946A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 519 Processing helix chain 'A' and resid 523 through 544 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 629 removed outlier: 3.605A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 660 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.830A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.668A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 779 No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 793 through 821 removed outlier: 3.553A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 857 removed outlier: 3.546A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 917 through 951 removed outlier: 3.585A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A 928 " --> pdb=" O MET A 924 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 929 " --> pdb=" O ILE A 925 " (cutoff:3.500A) Proline residue: A 930 - end of helix removed outlier: 3.919A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 951 " --> pdb=" O ASN A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 989 removed outlier: 3.690A pdb=" N ALA A 959 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 963 " --> pdb=" O PHE A 960 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 968 " --> pdb=" O PHE A 965 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 970 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 971 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 979 " --> pdb=" O GLY A 976 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 981 " --> pdb=" O VAL A 978 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 982 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP A 986 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1034 removed outlier: 3.633A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 483 through 488 removed outlier: 4.120A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.567A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 625 removed outlier: 4.042A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 641 No H-bonds generated for 'chain 'B' and resid 638 through 641' Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.817A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 removed outlier: 3.805A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 694 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.545A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.904A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 4.100A pdb=" N SER B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 820 removed outlier: 5.813A pdb=" N GLY B 794 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 795 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 798 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 800 " --> pdb=" O TYR B 797 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 801 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 804 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 806 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 813 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS B 815 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 817 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 819 " --> pdb=" O TYR B 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.524A pdb=" N HIS C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 483 through 488 removed outlier: 3.945A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 519 Processing helix chain 'C' and resid 523 through 544 Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 629 removed outlier: 3.605A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 641 Processing helix chain 'C' and resid 655 through 660 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.831A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 754 Processing helix chain 'C' and resid 758 through 769 removed outlier: 3.668A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 779 No H-bonds generated for 'chain 'C' and resid 776 through 779' Processing helix chain 'C' and resid 793 through 821 removed outlier: 3.553A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 857 removed outlier: 3.547A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 896 No H-bonds generated for 'chain 'C' and resid 894 through 896' Processing helix chain 'C' and resid 917 through 951 removed outlier: 3.585A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA C 928 " --> pdb=" O MET C 924 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR C 929 " --> pdb=" O ILE C 925 " (cutoff:3.500A) Proline residue: C 930 - end of helix removed outlier: 3.918A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 944 " --> pdb=" O PHE C 940 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 951 " --> pdb=" O ASN C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 989 removed outlier: 3.689A pdb=" N ALA C 959 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C 963 " --> pdb=" O PHE C 960 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 968 " --> pdb=" O PHE C 965 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 970 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 971 " --> pdb=" O LEU C 968 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 979 " --> pdb=" O GLY C 976 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 981 " --> pdb=" O VAL C 978 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER C 982 " --> pdb=" O LEU C 979 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP C 986 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1034 removed outlier: 3.633A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 488 removed outlier: 4.120A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 520 Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 523 through 546 removed outlier: 3.569A pdb=" N ARG D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 625 removed outlier: 4.042A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 641 No H-bonds generated for 'chain 'D' and resid 638 through 641' Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.816A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.805A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 694 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.544A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 755 Processing helix chain 'D' and resid 758 through 769 removed outlier: 3.905A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 removed outlier: 4.099A pdb=" N SER D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 820 removed outlier: 5.813A pdb=" N GLY D 794 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 795 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 798 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 800 " --> pdb=" O TYR D 797 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 801 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY D 804 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 806 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 813 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D 815 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 817 " --> pdb=" O PHE D 814 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 819 " --> pdb=" O TYR D 816 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= C, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.214A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 732 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.137A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 882 through 884 removed outlier: 3.634A pdb=" N LEU A 862 " --> pdb=" O SER A 884 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 867 through 869 Processing sheet with id= G, first strand: chain 'B' and resid 503 through 505 Processing sheet with id= H, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= I, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= J, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.214A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 732 " --> pdb=" O MET C 496 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.136A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.634A pdb=" N LEU C 862 " --> pdb=" O SER C 884 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 867 through 869 Processing sheet with id= N, first strand: chain 'D' and resid 503 through 505 694 hydrogen bonds defined for protein. 1818 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: 4.35 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2564 1.31 - 1.44: 4584 1.44 - 1.56: 9572 1.56 - 1.69: 152 1.69 - 1.81: 176 Bond restraints: 17048 Sorted by residual: bond pdb=" C05 QUS B1104 " pdb=" O19 QUS B1104 " ideal model delta sigma weight residual 1.185 1.449 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C05 QUS D1105 " pdb=" O19 QUS D1105 " ideal model delta sigma weight residual 1.185 1.449 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C05 QUS C1106 " pdb=" O19 QUS C1106 " ideal model delta sigma weight residual 1.185 1.447 -0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C05 QUS A1106 " pdb=" O19 QUS A1106 " ideal model delta sigma weight residual 1.185 1.446 -0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C04 QUS B1104 " pdb=" O18 QUS B1104 " ideal model delta sigma weight residual 1.185 1.413 -0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 17043 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.41: 296 105.41 - 112.58: 8660 112.58 - 119.74: 5567 119.74 - 126.90: 8157 126.90 - 134.07: 198 Bond angle restraints: 22878 Sorted by residual: angle pdb=" N ALA D 820 " pdb=" CA ALA D 820 " pdb=" C ALA D 820 " ideal model delta sigma weight residual 113.01 98.25 14.76 1.20e+00 6.94e-01 1.51e+02 angle pdb=" N ALA B 820 " pdb=" CA ALA B 820 " pdb=" C ALA B 820 " ideal model delta sigma weight residual 113.18 98.35 14.83 1.21e+00 6.83e-01 1.50e+02 angle pdb=" CA ARG B 819 " pdb=" C ARG B 819 " pdb=" N ALA B 820 " ideal model delta sigma weight residual 117.92 111.52 6.40 1.35e+00 5.49e-01 2.25e+01 angle pdb=" C GLY A 894 " pdb=" N GLU A 895 " pdb=" CA GLU A 895 " ideal model delta sigma weight residual 122.61 129.88 -7.27 1.56e+00 4.11e-01 2.17e+01 angle pdb=" C GLY C 894 " pdb=" N GLU C 895 " pdb=" CA GLU C 895 " ideal model delta sigma weight residual 122.61 129.86 -7.25 1.56e+00 4.11e-01 2.16e+01 ... (remaining 22873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 9830 35.75 - 71.50: 350 71.50 - 107.25: 32 107.25 - 143.00: 6 143.00 - 178.75: 8 Dihedral angle restraints: 10226 sinusoidal: 4360 harmonic: 5866 Sorted by residual: dihedral pdb=" CA LYS C 716 " pdb=" C LYS C 716 " pdb=" N PRO C 717 " pdb=" CA PRO C 717 " ideal model delta harmonic sigma weight residual 180.00 134.14 45.86 0 5.00e+00 4.00e-02 8.41e+01 dihedral pdb=" CA LYS A 716 " pdb=" C LYS A 716 " pdb=" N PRO A 717 " pdb=" CA PRO A 717 " ideal model delta harmonic sigma weight residual 180.00 134.15 45.85 0 5.00e+00 4.00e-02 8.41e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.27 -73.27 1 1.00e+01 1.00e-02 6.84e+01 ... (remaining 10223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2290 0.091 - 0.182: 170 0.182 - 0.274: 30 0.274 - 0.365: 2 0.365 - 0.456: 2 Chirality restraints: 2494 Sorted by residual: chirality pdb=" CG LEU C 892 " pdb=" CB LEU C 892 " pdb=" CD1 LEU C 892 " pdb=" CD2 LEU C 892 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CG LEU A 892 " pdb=" CB LEU A 892 " pdb=" CD1 LEU A 892 " pdb=" CD2 LEU A 892 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CA ALA B 820 " pdb=" N ALA B 820 " pdb=" C ALA B 820 " pdb=" CB ALA B 820 " both_signs ideal model delta sigma weight residual False 2.48 2.83 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 2491 not shown) Planarity restraints: 2774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 716 " 0.077 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO A 717 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO C 717 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 819 " -0.018 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C ARG B 819 " 0.066 2.00e-02 2.50e+03 pdb=" O ARG B 819 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA B 820 " -0.023 2.00e-02 2.50e+03 ... (remaining 2771 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3492 2.78 - 3.31: 15260 3.31 - 3.84: 26724 3.84 - 4.37: 31570 4.37 - 4.90: 52570 Nonbonded interactions: 129616 Sorted by model distance: nonbonded pdb=" O ARG D 692 " pdb=" OG SER D 696 " model vdw 2.246 2.440 nonbonded pdb=" O ARG B 692 " pdb=" OG SER B 696 " model vdw 2.247 2.440 nonbonded pdb=" O LEU B 639 " pdb=" OH TYR B 647 " model vdw 2.293 2.440 nonbonded pdb=" O LEU D 639 " pdb=" OH TYR D 647 " model vdw 2.293 2.440 nonbonded pdb=" OG SER D 706 " pdb=" OD1 ASN D 726 " model vdw 2.324 2.440 ... (remaining 129611 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 'C' } ncs_group { reference = (chain 'B' and (resid 394 through 823 or (resid 1101 and (name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23)) or resid 1102 through 1103)) selection = (chain 'D' and (resid 394 through 823 or resid 1101 or (resid 1102 through 1103 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or nam \ e C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or name C42 \ or name C43 or name C44 or name C45 or name C5 or name C6 or name C7 or name C8 \ or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3 \ P or name O4P or name P )))) } 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: 2.220 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: 10.720 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 43.540 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.011 0.264 17048 Z= 0.681 Angle : 1.268 14.825 22878 Z= 0.599 Chirality : 0.057 0.456 2494 Planarity : 0.007 0.118 2774 Dihedral : 17.496 178.748 6468 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 0.93 % Allowed : 5.28 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.13), residues: 2020 helix: -2.87 (0.09), residues: 1088 sheet: -2.11 (0.34), residues: 180 loop : -2.41 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 767 HIS 0.004 0.001 HIS C 883 PHE 0.042 0.002 PHE C 901 TYR 0.020 0.002 TYR A 768 ARG 0.008 0.001 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 617 time to evaluate : 1.923 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: A 418 ASN cc_start: 0.7583 (m-40) cc_final: 0.7087 (m-40) REVERT: A 427 ASP cc_start: 0.8542 (m-30) cc_final: 0.8327 (m-30) REVERT: A 537 SER cc_start: 0.8812 (m) cc_final: 0.8222 (t) REVERT: A 545 ARG cc_start: 0.7383 (mmt180) cc_final: 0.6343 (tpp-160) REVERT: A 799 LEU cc_start: 0.9094 (tp) cc_final: 0.8861 (tt) REVERT: A 835 LYS cc_start: 0.8189 (tppt) cc_final: 0.7634 (mmtt) REVERT: A 880 MET cc_start: 0.8642 (tmm) cc_final: 0.7968 (tmm) REVERT: A 985 ASN cc_start: 0.8835 (m-40) cc_final: 0.8490 (m-40) REVERT: B 407 MET cc_start: 0.4615 (mtm) cc_final: 0.4314 (mmm) REVERT: B 411 ASN cc_start: 0.8043 (m-40) cc_final: 0.7743 (m-40) REVERT: B 418 ASN cc_start: 0.7509 (p0) cc_final: 0.6209 (p0) REVERT: B 497 SER cc_start: 0.8293 (m) cc_final: 0.7899 (p) REVERT: B 503 MET cc_start: 0.7793 (ttt) cc_final: 0.7254 (tpp) REVERT: B 669 LYS cc_start: 0.9133 (mttt) cc_final: 0.8811 (mmtt) REVERT: B 702 TYR cc_start: 0.7772 (t80) cc_final: 0.7160 (t80) REVERT: B 709 ASN cc_start: 0.8509 (t0) cc_final: 0.7579 (t0) REVERT: B 710 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7914 (tp30) REVERT: B 715 ARG cc_start: 0.8039 (tpt-90) cc_final: 0.7718 (tmt-80) REVERT: B 756 GLN cc_start: 0.6367 (pt0) cc_final: 0.5796 (pm20) REVERT: C 427 ASP cc_start: 0.8444 (m-30) cc_final: 0.8208 (m-30) REVERT: C 461 ASN cc_start: 0.8531 (t0) cc_final: 0.8182 (p0) REVERT: C 519 ASP cc_start: 0.7813 (m-30) cc_final: 0.7524 (m-30) REVERT: C 527 MET cc_start: 0.8401 (ttm) cc_final: 0.8167 (ttm) REVERT: C 531 PHE cc_start: 0.8478 (m-10) cc_final: 0.8272 (m-10) REVERT: C 569 ASN cc_start: 0.7920 (t0) cc_final: 0.7288 (m-40) REVERT: C 577 LEU cc_start: 0.9192 (mm) cc_final: 0.8981 (mm) REVERT: C 613 ILE cc_start: 0.8862 (mt) cc_final: 0.8460 (mt) REVERT: C 835 LYS cc_start: 0.8303 (tppt) cc_final: 0.7897 (ttpt) REVERT: C 866 GLU cc_start: 0.6917 (tp30) cc_final: 0.6696 (tt0) REVERT: C 920 ASN cc_start: 0.8431 (t160) cc_final: 0.7814 (m-40) REVERT: C 924 MET cc_start: 0.8185 (mmt) cc_final: 0.7931 (mmp) REVERT: C 1013 SER cc_start: 0.8826 (t) cc_final: 0.8523 (p) REVERT: C 1023 MET cc_start: 0.8026 (mtp) cc_final: 0.7650 (mtp) REVERT: D 411 ASN cc_start: 0.7744 (m-40) cc_final: 0.7427 (m110) REVERT: D 460 TRP cc_start: 0.6804 (m100) cc_final: 0.6566 (m100) REVERT: D 524 GLU cc_start: 0.8354 (pm20) cc_final: 0.8015 (pm20) REVERT: D 544 SER cc_start: 0.8454 (m) cc_final: 0.7970 (t) REVERT: D 570 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7646 (mm-30) REVERT: D 609 THR cc_start: 0.9364 (p) cc_final: 0.9154 (t) REVERT: D 702 TYR cc_start: 0.7846 (t80) cc_final: 0.6952 (t80) REVERT: D 709 ASN cc_start: 0.8489 (t0) cc_final: 0.8263 (t0) REVERT: D 710 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 763 LYS cc_start: 0.9032 (tttt) cc_final: 0.8612 (tptt) REVERT: D 799 LEU cc_start: 0.9267 (tp) cc_final: 0.8979 (tt) outliers start: 16 outliers final: 6 residues processed: 632 average time/residue: 0.2836 time to fit residues: 264.1774 Evaluate side-chains 367 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 361 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 52 optimal weight: 0.0010 chunk 103 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 117 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 587 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN A 947 ASN A 950 HIS B 461 ASN B 587 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN D 586 GLN D 587 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 17048 Z= 0.179 Angle : 0.626 8.396 22878 Z= 0.329 Chirality : 0.043 0.225 2494 Planarity : 0.006 0.077 2774 Dihedral : 19.289 178.119 2782 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.23 % Allowed : 3.89 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.05 % 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: -1.58 (0.17), residues: 2020 helix: -0.15 (0.14), residues: 1102 sheet: -2.04 (0.32), residues: 204 loop : -2.05 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 766 HIS 0.003 0.001 HIS A 883 PHE 0.033 0.001 PHE C 901 TYR 0.024 0.002 TYR B 768 ARG 0.005 0.001 ARG C 899 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 479 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.8971 (m) cc_final: 0.8700 (m) REVERT: A 442 LEU cc_start: 0.8753 (mt) cc_final: 0.8423 (mt) REVERT: A 486 GLU cc_start: 0.9052 (pt0) cc_final: 0.8757 (pt0) REVERT: A 529 ILE cc_start: 0.9624 (mt) cc_final: 0.9424 (mt) REVERT: A 537 SER cc_start: 0.9048 (m) cc_final: 0.8649 (t) REVERT: A 637 GLU cc_start: 0.8518 (mp0) cc_final: 0.8288 (tm-30) REVERT: A 669 LYS cc_start: 0.9481 (ttpt) cc_final: 0.9128 (tttt) REVERT: A 835 LYS cc_start: 0.8523 (tppt) cc_final: 0.8156 (mmtt) REVERT: A 844 PHE cc_start: 0.8418 (m-80) cc_final: 0.8143 (m-80) REVERT: A 851 LEU cc_start: 0.8073 (tp) cc_final: 0.7783 (tp) REVERT: A 880 MET cc_start: 0.8138 (tmm) cc_final: 0.7144 (tmm) REVERT: A 892 LEU cc_start: 0.7716 (tp) cc_final: 0.7513 (tp) REVERT: A 924 MET cc_start: 0.7787 (mmm) cc_final: 0.6893 (mmt) REVERT: A 937 PHE cc_start: 0.8647 (t80) cc_final: 0.8150 (t80) REVERT: A 1023 MET cc_start: 0.8863 (mtp) cc_final: 0.8374 (mtp) REVERT: A 1029 MET cc_start: 0.7557 (mmp) cc_final: 0.7268 (mmm) REVERT: B 407 MET cc_start: 0.4555 (mtm) cc_final: 0.3963 (mmm) REVERT: B 411 ASN cc_start: 0.8250 (m-40) cc_final: 0.7876 (m-40) REVERT: B 418 ASN cc_start: 0.7473 (p0) cc_final: 0.6901 (p0) REVERT: B 501 SER cc_start: 0.9171 (t) cc_final: 0.8649 (p) REVERT: B 503 MET cc_start: 0.8043 (ttt) cc_final: 0.7839 (ttp) REVERT: B 669 LYS cc_start: 0.9090 (mttt) cc_final: 0.8871 (mmtt) REVERT: B 684 ARG cc_start: 0.8849 (tmt170) cc_final: 0.8582 (ptm-80) REVERT: B 702 TYR cc_start: 0.7744 (t80) cc_final: 0.7055 (t80) REVERT: C 425 CYS cc_start: 0.8755 (m) cc_final: 0.8547 (m) REVERT: C 461 ASN cc_start: 0.8487 (t0) cc_final: 0.8253 (p0) REVERT: C 502 ILE cc_start: 0.9484 (mp) cc_final: 0.9263 (mt) REVERT: C 519 ASP cc_start: 0.7512 (m-30) cc_final: 0.7185 (m-30) REVERT: C 527 MET cc_start: 0.8381 (ttm) cc_final: 0.8106 (ttm) REVERT: C 569 ASN cc_start: 0.7870 (t0) cc_final: 0.7124 (m-40) REVERT: C 573 ILE cc_start: 0.8989 (tp) cc_final: 0.8599 (tp) REVERT: C 577 LEU cc_start: 0.9368 (mm) cc_final: 0.9010 (mm) REVERT: C 604 VAL cc_start: 0.9613 (t) cc_final: 0.9412 (p) REVERT: C 675 ARG cc_start: 0.7675 (ptm160) cc_final: 0.7415 (ttm-80) REVERT: C 835 LYS cc_start: 0.8528 (tppt) cc_final: 0.8259 (ttpt) REVERT: C 866 GLU cc_start: 0.6599 (tp30) cc_final: 0.5941 (tt0) REVERT: C 880 MET cc_start: 0.8270 (tmm) cc_final: 0.7874 (tmm) REVERT: C 920 ASN cc_start: 0.8034 (t0) cc_final: 0.7747 (t0) REVERT: C 924 MET cc_start: 0.8072 (mmt) cc_final: 0.7545 (mmt) REVERT: C 1023 MET cc_start: 0.8308 (mtp) cc_final: 0.7873 (mtp) REVERT: D 411 ASN cc_start: 0.8008 (m-40) cc_final: 0.7506 (m110) REVERT: D 418 ASN cc_start: 0.7472 (p0) cc_final: 0.6576 (p0) REVERT: D 503 MET cc_start: 0.8303 (ttt) cc_final: 0.7813 (ttt) REVERT: D 524 GLU cc_start: 0.8479 (pm20) cc_final: 0.8272 (pm20) REVERT: D 537 SER cc_start: 0.9201 (p) cc_final: 0.8924 (t) REVERT: D 570 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7606 (mm-30) REVERT: D 702 TYR cc_start: 0.7890 (t80) cc_final: 0.6949 (t80) REVERT: D 710 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 714 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7735 (mm-40) REVERT: D 763 LYS cc_start: 0.9042 (tttt) cc_final: 0.8572 (tptt) REVERT: D 764 ASN cc_start: 0.8869 (m110) cc_final: 0.8603 (m110) REVERT: D 798 ILE cc_start: 0.9348 (mt) cc_final: 0.9102 (tp) REVERT: D 799 LEU cc_start: 0.9469 (tp) cc_final: 0.9114 (tt) outliers start: 4 outliers final: 0 residues processed: 482 average time/residue: 0.2569 time to fit residues: 188.8526 Evaluate side-chains 330 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 152 optimal weight: 0.8980 chunk 124 optimal weight: 0.0050 chunk 50 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 62 optimal weight: 0.0670 chunk 147 optimal weight: 2.9990 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN B 586 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 411 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN D 508 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17048 Z= 0.168 Angle : 0.596 8.762 22878 Z= 0.307 Chirality : 0.041 0.198 2494 Planarity : 0.005 0.073 2774 Dihedral : 18.162 179.200 2782 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.29 % Allowed : 3.19 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2020 helix: 0.74 (0.15), residues: 1072 sheet: -1.71 (0.32), residues: 222 loop : -1.78 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 766 HIS 0.002 0.001 HIS A 412 PHE 0.034 0.002 PHE A 999 TYR 0.014 0.001 TYR A 905 ARG 0.013 0.001 ARG A1031 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 448 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 GLU cc_start: 0.8449 (tp30) cc_final: 0.8214 (tp30) REVERT: A 442 LEU cc_start: 0.8822 (mt) cc_final: 0.8518 (mt) REVERT: A 486 GLU cc_start: 0.8936 (pt0) cc_final: 0.8697 (pt0) REVERT: A 528 CYS cc_start: 0.8755 (m) cc_final: 0.8476 (m) REVERT: A 537 SER cc_start: 0.9130 (m) cc_final: 0.8797 (t) REVERT: A 573 ILE cc_start: 0.9364 (tp) cc_final: 0.9092 (tp) REVERT: A 655 THR cc_start: 0.8637 (p) cc_final: 0.8325 (p) REVERT: A 669 LYS cc_start: 0.9543 (ttpt) cc_final: 0.9289 (ttpt) REVERT: A 808 LEU cc_start: 0.8930 (tt) cc_final: 0.8564 (mp) REVERT: A 835 LYS cc_start: 0.8490 (tppt) cc_final: 0.8109 (mmtt) REVERT: A 851 LEU cc_start: 0.8012 (tp) cc_final: 0.7740 (tp) REVERT: A 880 MET cc_start: 0.8094 (tmm) cc_final: 0.7367 (tmm) REVERT: A 892 LEU cc_start: 0.7602 (tp) cc_final: 0.7304 (tp) REVERT: A 937 PHE cc_start: 0.8675 (t80) cc_final: 0.8288 (t80) REVERT: A 1023 MET cc_start: 0.8778 (mtp) cc_final: 0.8382 (mtp) REVERT: B 407 MET cc_start: 0.4274 (mtm) cc_final: 0.4018 (mmp) REVERT: B 411 ASN cc_start: 0.8142 (m-40) cc_final: 0.7738 (m-40) REVERT: B 418 ASN cc_start: 0.7631 (p0) cc_final: 0.6873 (p0) REVERT: B 538 VAL cc_start: 0.9377 (t) cc_final: 0.9132 (t) REVERT: B 585 MET cc_start: 0.8875 (mmm) cc_final: 0.8351 (mmm) REVERT: B 641 LYS cc_start: 0.8370 (mptt) cc_final: 0.7477 (tppp) REVERT: B 669 LYS cc_start: 0.9112 (mttt) cc_final: 0.8905 (mmtt) REVERT: B 684 ARG cc_start: 0.8926 (tmt170) cc_final: 0.8718 (ttp80) REVERT: B 702 TYR cc_start: 0.7569 (t80) cc_final: 0.7026 (t80) REVERT: B 708 MET cc_start: 0.8723 (mtm) cc_final: 0.8508 (mtt) REVERT: B 714 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7736 (tt0) REVERT: B 747 ASN cc_start: 0.8926 (m110) cc_final: 0.8723 (m-40) REVERT: B 809 VAL cc_start: 0.8907 (m) cc_final: 0.8650 (m) REVERT: C 425 CYS cc_start: 0.8687 (m) cc_final: 0.8413 (m) REVERT: C 427 ASP cc_start: 0.8685 (m-30) cc_final: 0.8447 (m-30) REVERT: C 502 ILE cc_start: 0.9517 (mp) cc_final: 0.9155 (mt) REVERT: C 527 MET cc_start: 0.8465 (ttm) cc_final: 0.8159 (ttm) REVERT: C 569 ASN cc_start: 0.7743 (t0) cc_final: 0.6908 (m-40) REVERT: C 573 ILE cc_start: 0.9024 (tp) cc_final: 0.8671 (tp) REVERT: C 581 LEU cc_start: 0.8802 (tp) cc_final: 0.8554 (tp) REVERT: C 669 LYS cc_start: 0.9503 (ttpt) cc_final: 0.9268 (ttpt) REVERT: C 675 ARG cc_start: 0.7707 (ptm160) cc_final: 0.7292 (ptm160) REVERT: C 835 LYS cc_start: 0.8552 (tppt) cc_final: 0.8238 (ttpt) REVERT: C 866 GLU cc_start: 0.6645 (tp30) cc_final: 0.5683 (tt0) REVERT: C 880 MET cc_start: 0.8123 (tmm) cc_final: 0.7545 (tmm) REVERT: C 924 MET cc_start: 0.7979 (mmt) cc_final: 0.7655 (mmt) REVERT: C 955 ARG cc_start: 0.5183 (mmm-85) cc_final: 0.3261 (ttt-90) REVERT: C 1023 MET cc_start: 0.8307 (mtp) cc_final: 0.7990 (mtp) REVERT: D 411 ASN cc_start: 0.7956 (m-40) cc_final: 0.7478 (m110) REVERT: D 418 ASN cc_start: 0.7783 (p0) cc_final: 0.6866 (p0) REVERT: D 503 MET cc_start: 0.8535 (ttt) cc_final: 0.7412 (ttt) REVERT: D 537 SER cc_start: 0.9159 (p) cc_final: 0.8955 (t) REVERT: D 570 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7651 (mm-30) REVERT: D 702 TYR cc_start: 0.7771 (t80) cc_final: 0.6899 (t80) REVERT: D 763 LYS cc_start: 0.9041 (tttt) cc_final: 0.8607 (tttt) outliers start: 5 outliers final: 0 residues processed: 452 average time/residue: 0.2633 time to fit residues: 183.1192 Evaluate side-chains 319 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 0.0670 chunk 123 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN B 461 ASN B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 764 ASN C 435 HIS C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17048 Z= 0.232 Angle : 0.655 21.975 22878 Z= 0.341 Chirality : 0.044 0.402 2494 Planarity : 0.005 0.075 2774 Dihedral : 17.580 172.782 2782 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.35 % Allowed : 3.07 % Favored : 96.58 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 2020 helix: 1.03 (0.16), residues: 1076 sheet: -1.95 (0.33), residues: 206 loop : -1.71 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 767 HIS 0.003 0.001 HIS A 954 PHE 0.043 0.002 PHE A 938 TYR 0.016 0.002 TYR B 700 ARG 0.005 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 407 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.8737 (mt) cc_final: 0.8423 (mt) REVERT: A 486 GLU cc_start: 0.9145 (pt0) cc_final: 0.8807 (pt0) REVERT: A 528 CYS cc_start: 0.8699 (m) cc_final: 0.8496 (m) REVERT: A 537 SER cc_start: 0.9129 (m) cc_final: 0.8579 (t) REVERT: A 669 LYS cc_start: 0.9557 (ttpt) cc_final: 0.9278 (ttpt) REVERT: A 808 LEU cc_start: 0.8934 (tt) cc_final: 0.8539 (mp) REVERT: A 835 LYS cc_start: 0.8456 (tppt) cc_final: 0.8140 (mmtt) REVERT: A 851 LEU cc_start: 0.7961 (tp) cc_final: 0.7734 (tp) REVERT: A 899 ARG cc_start: 0.5406 (ptp-170) cc_final: 0.4695 (tpm170) REVERT: A 924 MET cc_start: 0.7903 (mmm) cc_final: 0.6963 (mmt) REVERT: A 937 PHE cc_start: 0.8724 (t80) cc_final: 0.8331 (t80) REVERT: A 947 ASN cc_start: 0.8452 (m110) cc_final: 0.8131 (m110) REVERT: A 1023 MET cc_start: 0.8735 (mtp) cc_final: 0.8486 (mtp) REVERT: B 407 MET cc_start: 0.3611 (mtm) cc_final: 0.3404 (mmm) REVERT: B 408 MET cc_start: 0.5537 (tpt) cc_final: 0.4778 (mmm) REVERT: B 411 ASN cc_start: 0.8096 (m-40) cc_final: 0.7557 (m-40) REVERT: B 527 MET cc_start: 0.7587 (tpp) cc_final: 0.7164 (mmt) REVERT: B 531 PHE cc_start: 0.8490 (m-10) cc_final: 0.8205 (m-10) REVERT: B 604 VAL cc_start: 0.9788 (m) cc_final: 0.9560 (p) REVERT: B 669 LYS cc_start: 0.9158 (mttt) cc_final: 0.8936 (mmtt) REVERT: B 702 TYR cc_start: 0.7871 (t80) cc_final: 0.6948 (t80) REVERT: B 708 MET cc_start: 0.8704 (mtm) cc_final: 0.8446 (mtt) REVERT: B 714 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7719 (tt0) REVERT: B 747 ASN cc_start: 0.8916 (m110) cc_final: 0.8604 (m110) REVERT: C 427 ASP cc_start: 0.8705 (m-30) cc_final: 0.8490 (m-30) REVERT: C 502 ILE cc_start: 0.9570 (mp) cc_final: 0.9360 (mt) REVERT: C 503 MET cc_start: 0.8610 (ttm) cc_final: 0.7939 (ttp) REVERT: C 527 MET cc_start: 0.8556 (ttm) cc_final: 0.8299 (ttm) REVERT: C 528 CYS cc_start: 0.8407 (m) cc_final: 0.8180 (m) REVERT: C 569 ASN cc_start: 0.7644 (t0) cc_final: 0.6919 (m-40) REVERT: C 585 MET cc_start: 0.9197 (mmm) cc_final: 0.8706 (mmm) REVERT: C 675 ARG cc_start: 0.7718 (ptm160) cc_final: 0.7351 (ptm160) REVERT: C 815 CYS cc_start: 0.7271 (m) cc_final: 0.6247 (p) REVERT: C 835 LYS cc_start: 0.8576 (tppt) cc_final: 0.8318 (ttpt) REVERT: C 866 GLU cc_start: 0.6701 (tp30) cc_final: 0.6460 (tp30) REVERT: C 924 MET cc_start: 0.8100 (mmt) cc_final: 0.7707 (mmt) REVERT: C 938 PHE cc_start: 0.7583 (m-80) cc_final: 0.7348 (m-80) REVERT: C 950 HIS cc_start: 0.6211 (m170) cc_final: 0.5856 (t-90) REVERT: C 955 ARG cc_start: 0.5139 (mmm-85) cc_final: 0.3320 (ptt-90) REVERT: C 1005 TRP cc_start: 0.5932 (t-100) cc_final: 0.5619 (t-100) REVERT: C 1013 SER cc_start: 0.9074 (t) cc_final: 0.8649 (p) REVERT: C 1023 MET cc_start: 0.8335 (mtp) cc_final: 0.7896 (mtp) REVERT: D 408 MET cc_start: 0.4845 (mmm) cc_final: 0.4565 (mmm) REVERT: D 411 ASN cc_start: 0.7940 (m-40) cc_final: 0.7448 (m110) REVERT: D 503 MET cc_start: 0.8863 (ttt) cc_final: 0.8516 (ttt) REVERT: D 570 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7560 (mm-30) REVERT: D 702 TYR cc_start: 0.7806 (t80) cc_final: 0.6736 (t80) REVERT: D 709 ASN cc_start: 0.8650 (t0) cc_final: 0.7834 (m-40) REVERT: D 744 THR cc_start: 0.8086 (m) cc_final: 0.7881 (p) outliers start: 6 outliers final: 0 residues processed: 411 average time/residue: 0.2487 time to fit residues: 159.0199 Evaluate side-chains 296 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 166 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 764 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17048 Z= 0.265 Angle : 0.687 22.740 22878 Z= 0.356 Chirality : 0.045 0.412 2494 Planarity : 0.005 0.075 2774 Dihedral : 17.180 163.426 2782 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.23 % Allowed : 3.65 % Favored : 96.11 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 2020 helix: 1.10 (0.16), residues: 1078 sheet: -2.00 (0.34), residues: 186 loop : -1.82 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 460 HIS 0.004 0.001 HIS A 954 PHE 0.037 0.002 PHE A 901 TYR 0.020 0.002 TYR B 647 ARG 0.007 0.001 ARG A1031 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 386 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8618 (t80) cc_final: 0.8334 (t80) REVERT: A 427 ASP cc_start: 0.8852 (m-30) cc_final: 0.8639 (m-30) REVERT: A 486 GLU cc_start: 0.8962 (pt0) cc_final: 0.8707 (pt0) REVERT: A 537 SER cc_start: 0.9129 (m) cc_final: 0.8580 (t) REVERT: A 585 MET cc_start: 0.9261 (mmm) cc_final: 0.9054 (mmm) REVERT: A 763 LYS cc_start: 0.8551 (tptp) cc_final: 0.7976 (tptt) REVERT: A 808 LEU cc_start: 0.8938 (tt) cc_final: 0.8504 (mp) REVERT: A 835 LYS cc_start: 0.8444 (tppt) cc_final: 0.8148 (mmtt) REVERT: A 880 MET cc_start: 0.8032 (tmm) cc_final: 0.7745 (tmm) REVERT: A 924 MET cc_start: 0.7934 (mmm) cc_final: 0.7018 (mmt) REVERT: A 937 PHE cc_start: 0.8772 (t80) cc_final: 0.8418 (t80) REVERT: A 947 ASN cc_start: 0.8464 (m110) cc_final: 0.8075 (m110) REVERT: A 1023 MET cc_start: 0.8673 (mtp) cc_final: 0.8393 (mtp) REVERT: B 407 MET cc_start: 0.4045 (mtm) cc_final: 0.3662 (mmm) REVERT: B 408 MET cc_start: 0.5455 (tpt) cc_final: 0.4916 (mmm) REVERT: B 411 ASN cc_start: 0.7937 (m-40) cc_final: 0.7428 (m-40) REVERT: B 418 ASN cc_start: 0.7389 (p0) cc_final: 0.6601 (p0) REVERT: B 604 VAL cc_start: 0.9794 (m) cc_final: 0.9583 (p) REVERT: B 669 LYS cc_start: 0.9169 (mttt) cc_final: 0.8956 (mmtt) REVERT: B 710 GLU cc_start: 0.8661 (tp30) cc_final: 0.8415 (tp30) REVERT: B 714 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7488 (tt0) REVERT: B 747 ASN cc_start: 0.8856 (m110) cc_final: 0.8541 (m110) REVERT: C 425 CYS cc_start: 0.8729 (m) cc_final: 0.8437 (m) REVERT: C 427 ASP cc_start: 0.8691 (m-30) cc_final: 0.8456 (m-30) REVERT: C 502 ILE cc_start: 0.9569 (mp) cc_final: 0.9360 (mt) REVERT: C 519 ASP cc_start: 0.7556 (m-30) cc_final: 0.7351 (m-30) REVERT: C 527 MET cc_start: 0.8625 (ttm) cc_final: 0.8425 (ttm) REVERT: C 569 ASN cc_start: 0.7759 (t0) cc_final: 0.7194 (m-40) REVERT: C 573 ILE cc_start: 0.9310 (tp) cc_final: 0.9051 (tp) REVERT: C 813 GLU cc_start: 0.9055 (pp20) cc_final: 0.8372 (tt0) REVERT: C 815 CYS cc_start: 0.7303 (m) cc_final: 0.6182 (p) REVERT: C 880 MET cc_start: 0.8095 (tmm) cc_final: 0.7798 (tmm) REVERT: C 938 PHE cc_start: 0.7651 (m-80) cc_final: 0.7323 (m-80) REVERT: C 950 HIS cc_start: 0.6265 (m170) cc_final: 0.5644 (t-90) REVERT: C 955 ARG cc_start: 0.5264 (mmm-85) cc_final: 0.3455 (ptt-90) REVERT: C 1005 TRP cc_start: 0.6182 (t-100) cc_final: 0.5762 (t-100) REVERT: C 1009 PHE cc_start: 0.8484 (m-10) cc_final: 0.8177 (m-10) REVERT: C 1023 MET cc_start: 0.8379 (mtp) cc_final: 0.8002 (mtp) REVERT: D 408 MET cc_start: 0.4625 (mmm) cc_final: 0.4373 (mmm) REVERT: D 411 ASN cc_start: 0.7747 (m-40) cc_final: 0.7283 (m-40) REVERT: D 464 VAL cc_start: 0.8763 (m) cc_final: 0.8554 (m) REVERT: D 503 MET cc_start: 0.8745 (ttt) cc_final: 0.8536 (tpp) REVERT: D 570 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7639 (mm-30) REVERT: D 591 ILE cc_start: 0.8660 (mm) cc_final: 0.8359 (tt) REVERT: D 747 ASN cc_start: 0.8808 (m110) cc_final: 0.8563 (m110) outliers start: 4 outliers final: 0 residues processed: 388 average time/residue: 0.2377 time to fit residues: 146.6938 Evaluate side-chains 296 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 764 ASN C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN D 764 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17048 Z= 0.318 Angle : 0.709 17.757 22878 Z= 0.366 Chirality : 0.045 0.339 2494 Planarity : 0.005 0.077 2774 Dihedral : 17.053 162.928 2782 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.12 % Allowed : 3.19 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 2020 helix: 1.07 (0.16), residues: 1066 sheet: -2.14 (0.32), residues: 208 loop : -1.81 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 460 HIS 0.012 0.002 HIS D 412 PHE 0.035 0.002 PHE A1009 TYR 0.018 0.002 TYR D 732 ARG 0.007 0.001 ARG A1031 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 346 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8743 (t80) cc_final: 0.8522 (t80) REVERT: A 427 ASP cc_start: 0.8871 (m-30) cc_final: 0.8664 (m-30) REVERT: A 503 MET cc_start: 0.8930 (tmm) cc_final: 0.8552 (tmm) REVERT: A 537 SER cc_start: 0.9136 (m) cc_final: 0.8553 (t) REVERT: A 669 LYS cc_start: 0.9540 (ttpt) cc_final: 0.9315 (tttt) REVERT: A 808 LEU cc_start: 0.8952 (tt) cc_final: 0.8531 (mp) REVERT: A 840 LEU cc_start: 0.8562 (mt) cc_final: 0.8192 (mt) REVERT: A 844 PHE cc_start: 0.8376 (m-80) cc_final: 0.8125 (m-80) REVERT: A 874 GLN cc_start: 0.7127 (pt0) cc_final: 0.6910 (pt0) REVERT: A 880 MET cc_start: 0.8152 (tmm) cc_final: 0.7950 (tmm) REVERT: A 920 ASN cc_start: 0.8134 (m110) cc_final: 0.7839 (m110) REVERT: A 924 MET cc_start: 0.7964 (mmm) cc_final: 0.7065 (mmt) REVERT: A 937 PHE cc_start: 0.8794 (t80) cc_final: 0.8465 (t80) REVERT: A 947 ASN cc_start: 0.8534 (m110) cc_final: 0.8145 (m110) REVERT: A 1023 MET cc_start: 0.8667 (mtp) cc_final: 0.8340 (mtp) REVERT: B 407 MET cc_start: 0.4025 (mtm) cc_final: 0.3715 (mmm) REVERT: B 408 MET cc_start: 0.5550 (tpt) cc_final: 0.5017 (mmm) REVERT: B 411 ASN cc_start: 0.7941 (m-40) cc_final: 0.7481 (m-40) REVERT: B 544 SER cc_start: 0.9026 (m) cc_final: 0.8749 (t) REVERT: B 604 VAL cc_start: 0.9804 (m) cc_final: 0.9604 (p) REVERT: B 670 MET cc_start: 0.9040 (mmp) cc_final: 0.8840 (mmp) REVERT: B 710 GLU cc_start: 0.8716 (tp30) cc_final: 0.8480 (tp30) REVERT: B 714 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7591 (tt0) REVERT: B 744 THR cc_start: 0.7920 (m) cc_final: 0.7697 (m) REVERT: B 747 ASN cc_start: 0.8816 (m110) cc_final: 0.8515 (m110) REVERT: C 425 CYS cc_start: 0.8733 (m) cc_final: 0.8519 (m) REVERT: C 502 ILE cc_start: 0.9608 (mp) cc_final: 0.9402 (mt) REVERT: C 519 ASP cc_start: 0.7629 (m-30) cc_final: 0.7387 (m-30) REVERT: C 527 MET cc_start: 0.8609 (ttm) cc_final: 0.8392 (ttm) REVERT: C 813 GLU cc_start: 0.9019 (pp20) cc_final: 0.8547 (tt0) REVERT: C 815 CYS cc_start: 0.7712 (m) cc_final: 0.6487 (p) REVERT: C 880 MET cc_start: 0.8125 (tmm) cc_final: 0.7724 (tmm) REVERT: C 938 PHE cc_start: 0.7707 (m-80) cc_final: 0.7285 (m-80) REVERT: C 950 HIS cc_start: 0.6566 (m170) cc_final: 0.6301 (m-70) REVERT: C 955 ARG cc_start: 0.5207 (mmm-85) cc_final: 0.3387 (ptt90) REVERT: C 1005 TRP cc_start: 0.6456 (t-100) cc_final: 0.5866 (t-100) REVERT: C 1009 PHE cc_start: 0.8421 (m-10) cc_final: 0.8108 (m-10) REVERT: C 1013 SER cc_start: 0.9229 (t) cc_final: 0.8995 (p) REVERT: C 1023 MET cc_start: 0.8527 (mtp) cc_final: 0.8129 (mtp) REVERT: D 503 MET cc_start: 0.8552 (ttt) cc_final: 0.8265 (ttt) REVERT: D 570 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7454 (mm-30) REVERT: D 591 ILE cc_start: 0.8547 (mm) cc_final: 0.8235 (tt) outliers start: 2 outliers final: 0 residues processed: 348 average time/residue: 0.2403 time to fit residues: 132.6736 Evaluate side-chains 263 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 164 optimal weight: 0.3980 chunk 109 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN B 461 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN B 764 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN D 461 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17048 Z= 0.177 Angle : 0.632 21.629 22878 Z= 0.321 Chirality : 0.043 0.398 2494 Planarity : 0.005 0.075 2774 Dihedral : 16.082 167.125 2782 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 2020 helix: 1.38 (0.16), residues: 1064 sheet: -2.14 (0.32), residues: 208 loop : -1.60 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 460 HIS 0.003 0.001 HIS A 883 PHE 0.050 0.001 PHE A 901 TYR 0.017 0.001 TYR D 700 ARG 0.004 0.000 ARG A1031 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.7745 (m-30) cc_final: 0.7450 (m-30) REVERT: A 529 ILE cc_start: 0.9589 (mt) cc_final: 0.9378 (mt) REVERT: A 537 SER cc_start: 0.9178 (m) cc_final: 0.8461 (t) REVERT: A 581 LEU cc_start: 0.9025 (tp) cc_final: 0.8822 (tp) REVERT: A 655 THR cc_start: 0.8669 (p) cc_final: 0.8444 (p) REVERT: A 669 LYS cc_start: 0.9545 (ttpt) cc_final: 0.9330 (tttt) REVERT: A 808 LEU cc_start: 0.8811 (tt) cc_final: 0.8412 (mp) REVERT: A 880 MET cc_start: 0.8028 (tmm) cc_final: 0.7468 (tmm) REVERT: A 920 ASN cc_start: 0.8137 (m110) cc_final: 0.7855 (m110) REVERT: A 924 MET cc_start: 0.7893 (mmm) cc_final: 0.7182 (mmt) REVERT: A 937 PHE cc_start: 0.8792 (t80) cc_final: 0.8443 (t80) REVERT: A 947 ASN cc_start: 0.8548 (m-40) cc_final: 0.8088 (m-40) REVERT: A 1023 MET cc_start: 0.8760 (mtp) cc_final: 0.8504 (mtp) REVERT: B 399 THR cc_start: 0.7436 (m) cc_final: 0.7106 (p) REVERT: B 408 MET cc_start: 0.5527 (tpt) cc_final: 0.4933 (mmm) REVERT: B 411 ASN cc_start: 0.8013 (m-40) cc_final: 0.7555 (m-40) REVERT: B 463 MET cc_start: 0.7748 (mmm) cc_final: 0.7262 (mmt) REVERT: B 544 SER cc_start: 0.8992 (m) cc_final: 0.8778 (t) REVERT: B 585 MET cc_start: 0.8834 (mmm) cc_final: 0.8559 (mmm) REVERT: B 669 LYS cc_start: 0.9136 (mttt) cc_final: 0.8917 (mmtt) REVERT: B 710 GLU cc_start: 0.8637 (tp30) cc_final: 0.8437 (tp30) REVERT: B 714 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7444 (tt0) REVERT: B 726 ASN cc_start: 0.8743 (m-40) cc_final: 0.8511 (m110) REVERT: B 747 ASN cc_start: 0.8773 (m110) cc_final: 0.8461 (m110) REVERT: C 427 ASP cc_start: 0.8686 (m-30) cc_final: 0.8482 (m-30) REVERT: C 502 ILE cc_start: 0.9601 (mp) cc_final: 0.9381 (mt) REVERT: C 519 ASP cc_start: 0.7578 (m-30) cc_final: 0.7336 (m-30) REVERT: C 527 MET cc_start: 0.8601 (ttm) cc_final: 0.8396 (ttm) REVERT: C 655 THR cc_start: 0.8586 (p) cc_final: 0.8377 (p) REVERT: C 708 MET cc_start: 0.8926 (mpp) cc_final: 0.8708 (mtm) REVERT: C 748 LEU cc_start: 0.8503 (mm) cc_final: 0.7959 (pp) REVERT: C 813 GLU cc_start: 0.8968 (pp20) cc_final: 0.8572 (tt0) REVERT: C 815 CYS cc_start: 0.7650 (m) cc_final: 0.6417 (p) REVERT: C 840 LEU cc_start: 0.7907 (tp) cc_final: 0.7635 (tp) REVERT: C 844 PHE cc_start: 0.8033 (m-80) cc_final: 0.7747 (m-80) REVERT: C 880 MET cc_start: 0.8011 (tmm) cc_final: 0.7563 (tmm) REVERT: C 924 MET cc_start: 0.8107 (mmt) cc_final: 0.7482 (mmt) REVERT: C 950 HIS cc_start: 0.6505 (m170) cc_final: 0.5757 (t-90) REVERT: C 955 ARG cc_start: 0.5104 (mmm-85) cc_final: 0.3333 (ptt90) REVERT: C 1005 TRP cc_start: 0.6152 (t-100) cc_final: 0.5439 (t-100) REVERT: C 1013 SER cc_start: 0.9224 (t) cc_final: 0.8947 (p) REVERT: C 1023 MET cc_start: 0.8484 (mtp) cc_final: 0.7899 (mtt) REVERT: D 529 ILE cc_start: 0.9665 (mp) cc_final: 0.9449 (mp) REVERT: D 570 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7555 (mm-30) REVERT: D 591 ILE cc_start: 0.8934 (mm) cc_final: 0.8673 (pt) REVERT: D 714 GLN cc_start: 0.8425 (mm-40) cc_final: 0.7993 (pt0) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.2310 time to fit residues: 141.1993 Evaluate side-chains 280 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.0980 chunk 123 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 0.1980 chunk 153 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN B 461 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 435 HIS C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN D 461 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17048 Z= 0.229 Angle : 0.668 18.372 22878 Z= 0.341 Chirality : 0.044 0.339 2494 Planarity : 0.005 0.078 2774 Dihedral : 15.862 169.925 2782 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 2020 helix: 1.20 (0.16), residues: 1074 sheet: -2.20 (0.31), residues: 220 loop : -1.69 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 460 HIS 0.005 0.001 HIS A 883 PHE 0.057 0.002 PHE A 901 TYR 0.033 0.002 TYR A 732 ARG 0.004 0.000 ARG C 897 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.8777 (m-30) cc_final: 0.8557 (m-30) REVERT: A 519 ASP cc_start: 0.7698 (m-30) cc_final: 0.7410 (m-30) REVERT: A 537 SER cc_start: 0.9114 (m) cc_final: 0.8578 (t) REVERT: A 655 THR cc_start: 0.8750 (p) cc_final: 0.8535 (p) REVERT: A 669 LYS cc_start: 0.9533 (ttpt) cc_final: 0.9321 (tttt) REVERT: A 808 LEU cc_start: 0.8863 (tt) cc_final: 0.8441 (mp) REVERT: A 874 GLN cc_start: 0.7310 (pt0) cc_final: 0.7062 (pt0) REVERT: A 880 MET cc_start: 0.7997 (tmm) cc_final: 0.7604 (tmm) REVERT: A 920 ASN cc_start: 0.8302 (m110) cc_final: 0.7419 (t0) REVERT: A 937 PHE cc_start: 0.8820 (t80) cc_final: 0.8438 (t80) REVERT: A 947 ASN cc_start: 0.8624 (m110) cc_final: 0.8224 (m110) REVERT: A 1023 MET cc_start: 0.8721 (mtp) cc_final: 0.8392 (mtp) REVERT: B 411 ASN cc_start: 0.7912 (m-40) cc_final: 0.7457 (m-40) REVERT: B 496 MET cc_start: 0.7601 (ptp) cc_final: 0.6917 (pmm) REVERT: B 585 MET cc_start: 0.8884 (mmm) cc_final: 0.8651 (mmm) REVERT: B 669 LYS cc_start: 0.9128 (mttt) cc_final: 0.8839 (mmtt) REVERT: B 710 GLU cc_start: 0.8673 (tp30) cc_final: 0.8466 (tp30) REVERT: B 714 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7492 (tt0) REVERT: B 744 THR cc_start: 0.7946 (m) cc_final: 0.7729 (m) REVERT: B 747 ASN cc_start: 0.8844 (m110) cc_final: 0.8486 (m110) REVERT: C 519 ASP cc_start: 0.7540 (m-30) cc_final: 0.7319 (m-30) REVERT: C 527 MET cc_start: 0.8708 (ttm) cc_final: 0.8454 (ttm) REVERT: C 748 LEU cc_start: 0.8516 (mm) cc_final: 0.7958 (pp) REVERT: C 756 GLN cc_start: 0.7765 (mp10) cc_final: 0.7288 (tm-30) REVERT: C 807 MET cc_start: 0.9031 (mmm) cc_final: 0.8712 (mmm) REVERT: C 813 GLU cc_start: 0.8992 (pp20) cc_final: 0.8617 (tt0) REVERT: C 815 CYS cc_start: 0.7632 (m) cc_final: 0.6465 (p) REVERT: C 844 PHE cc_start: 0.8126 (m-80) cc_final: 0.7854 (m-80) REVERT: C 938 PHE cc_start: 0.7812 (m-10) cc_final: 0.7575 (m-80) REVERT: C 950 HIS cc_start: 0.6649 (m170) cc_final: 0.5794 (t-90) REVERT: C 955 ARG cc_start: 0.5120 (mmm-85) cc_final: 0.3424 (ptt90) REVERT: C 1005 TRP cc_start: 0.6186 (t-100) cc_final: 0.5469 (t-100) REVERT: C 1013 SER cc_start: 0.9267 (t) cc_final: 0.9041 (p) REVERT: C 1023 MET cc_start: 0.8601 (mtp) cc_final: 0.7940 (mtt) REVERT: D 408 MET cc_start: 0.5458 (mmm) cc_final: 0.5214 (tpt) REVERT: D 529 ILE cc_start: 0.9675 (mp) cc_final: 0.9443 (mp) REVERT: D 570 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7653 (mm-30) REVERT: D 591 ILE cc_start: 0.8856 (mm) cc_final: 0.8618 (pt) REVERT: D 714 GLN cc_start: 0.8433 (mm-40) cc_final: 0.7904 (pt0) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.2358 time to fit residues: 134.7671 Evaluate side-chains 271 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN D 461 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17048 Z= 0.247 Angle : 0.670 16.108 22878 Z= 0.341 Chirality : 0.044 0.293 2494 Planarity : 0.005 0.079 2774 Dihedral : 15.667 173.251 2782 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 2020 helix: 1.18 (0.16), residues: 1068 sheet: -2.20 (0.32), residues: 198 loop : -1.74 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 460 HIS 0.006 0.001 HIS A 883 PHE 0.051 0.002 PHE A 901 TYR 0.025 0.002 TYR A 732 ARG 0.005 0.000 ARG C 897 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 1.963 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: A 427 ASP cc_start: 0.8760 (m-30) cc_final: 0.8539 (m-30) REVERT: A 503 MET cc_start: 0.8794 (ttt) cc_final: 0.8256 (tmm) REVERT: A 519 ASP cc_start: 0.7682 (m-30) cc_final: 0.7410 (m-30) REVERT: A 537 SER cc_start: 0.9120 (m) cc_final: 0.8606 (t) REVERT: A 585 MET cc_start: 0.9183 (mmm) cc_final: 0.8585 (mmm) REVERT: A 655 THR cc_start: 0.8792 (p) cc_final: 0.8576 (p) REVERT: A 669 LYS cc_start: 0.9539 (ttpt) cc_final: 0.9334 (tttt) REVERT: A 808 LEU cc_start: 0.8809 (tt) cc_final: 0.8442 (mp) REVERT: A 874 GLN cc_start: 0.7215 (pt0) cc_final: 0.6979 (pt0) REVERT: A 880 MET cc_start: 0.8069 (tmm) cc_final: 0.7541 (tmm) REVERT: A 937 PHE cc_start: 0.8727 (t80) cc_final: 0.8327 (t80) REVERT: A 1023 MET cc_start: 0.8655 (mtp) cc_final: 0.8357 (mtp) REVERT: B 408 MET cc_start: 0.4682 (mmm) cc_final: 0.4261 (tpt) REVERT: B 411 ASN cc_start: 0.7899 (m-40) cc_final: 0.7437 (m-40) REVERT: B 463 MET cc_start: 0.7716 (mmm) cc_final: 0.7340 (mmt) REVERT: B 496 MET cc_start: 0.7684 (ptp) cc_final: 0.7065 (pmm) REVERT: B 585 MET cc_start: 0.8904 (mmm) cc_final: 0.8633 (mmm) REVERT: B 591 ILE cc_start: 0.8863 (mm) cc_final: 0.8646 (pt) REVERT: B 714 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7417 (tt0) REVERT: B 744 THR cc_start: 0.7920 (m) cc_final: 0.7684 (m) REVERT: B 747 ASN cc_start: 0.8821 (m110) cc_final: 0.8495 (m110) REVERT: C 424 TYR cc_start: 0.8411 (t80) cc_final: 0.8205 (t80) REVERT: C 425 CYS cc_start: 0.8769 (m) cc_final: 0.8416 (m) REVERT: C 519 ASP cc_start: 0.7598 (m-30) cc_final: 0.7361 (m-30) REVERT: C 527 MET cc_start: 0.8698 (ttm) cc_final: 0.8469 (ttm) REVERT: C 655 THR cc_start: 0.8669 (p) cc_final: 0.8456 (p) REVERT: C 748 LEU cc_start: 0.8518 (mm) cc_final: 0.7974 (pp) REVERT: C 756 GLN cc_start: 0.7904 (mp10) cc_final: 0.7324 (tm-30) REVERT: C 807 MET cc_start: 0.9000 (mmm) cc_final: 0.8661 (mmm) REVERT: C 813 GLU cc_start: 0.8962 (pp20) cc_final: 0.8628 (tt0) REVERT: C 815 CYS cc_start: 0.7655 (m) cc_final: 0.6484 (p) REVERT: C 924 MET cc_start: 0.8055 (mmt) cc_final: 0.7505 (mmt) REVERT: C 938 PHE cc_start: 0.7757 (m-10) cc_final: 0.7515 (m-80) REVERT: C 950 HIS cc_start: 0.6736 (m170) cc_final: 0.6450 (m-70) REVERT: C 955 ARG cc_start: 0.5037 (mmm-85) cc_final: 0.3369 (ptt90) REVERT: C 1005 TRP cc_start: 0.6271 (t-100) cc_final: 0.5492 (t60) REVERT: C 1023 MET cc_start: 0.8537 (mtp) cc_final: 0.7915 (mtm) REVERT: D 585 MET cc_start: 0.8908 (mmm) cc_final: 0.8299 (ttm) REVERT: D 591 ILE cc_start: 0.8780 (mm) cc_final: 0.8529 (pt) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2379 time to fit residues: 131.8598 Evaluate side-chains 266 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 0.2980 chunk 191 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN B 461 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17048 Z= 0.194 Angle : 0.645 14.797 22878 Z= 0.327 Chirality : 0.043 0.275 2494 Planarity : 0.005 0.079 2774 Dihedral : 15.211 176.168 2782 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 2020 helix: 1.25 (0.16), residues: 1074 sheet: -2.21 (0.31), residues: 220 loop : -1.66 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 767 HIS 0.004 0.001 HIS A 883 PHE 0.051 0.002 PHE A 901 TYR 0.019 0.001 TYR A 732 ARG 0.003 0.000 ARG A1031 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8003 (ptmt) REVERT: A 487 GLU cc_start: 0.8814 (pp20) cc_final: 0.8607 (pp20) REVERT: A 519 ASP cc_start: 0.7649 (m-30) cc_final: 0.7374 (m-30) REVERT: A 537 SER cc_start: 0.9081 (m) cc_final: 0.8575 (t) REVERT: A 655 THR cc_start: 0.8802 (p) cc_final: 0.8582 (p) REVERT: A 670 MET cc_start: 0.9225 (ptp) cc_final: 0.9004 (ptp) REVERT: A 808 LEU cc_start: 0.8755 (tt) cc_final: 0.8410 (mp) REVERT: A 844 PHE cc_start: 0.8164 (m-80) cc_final: 0.7869 (m-80) REVERT: A 880 MET cc_start: 0.7997 (tmm) cc_final: 0.7552 (tmm) REVERT: A 937 PHE cc_start: 0.8719 (t80) cc_final: 0.8322 (t80) REVERT: A 1023 MET cc_start: 0.8644 (mtp) cc_final: 0.8289 (mtp) REVERT: B 408 MET cc_start: 0.4936 (mmm) cc_final: 0.4582 (tpt) REVERT: B 411 ASN cc_start: 0.7960 (m-40) cc_final: 0.7501 (m-40) REVERT: B 585 MET cc_start: 0.8823 (mmm) cc_final: 0.8570 (mmm) REVERT: B 669 LYS cc_start: 0.9137 (mttt) cc_final: 0.8813 (mmtt) REVERT: B 710 GLU cc_start: 0.8601 (tp30) cc_final: 0.8308 (tp30) REVERT: B 714 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7379 (tt0) REVERT: B 747 ASN cc_start: 0.8808 (m110) cc_final: 0.8482 (m110) REVERT: C 519 ASP cc_start: 0.7603 (m-30) cc_final: 0.7380 (m-30) REVERT: C 527 MET cc_start: 0.8693 (ttm) cc_final: 0.8481 (ttm) REVERT: C 655 THR cc_start: 0.8637 (p) cc_final: 0.8433 (p) REVERT: C 748 LEU cc_start: 0.8494 (mm) cc_final: 0.7975 (pp) REVERT: C 756 GLN cc_start: 0.7789 (mp10) cc_final: 0.7248 (tm-30) REVERT: C 807 MET cc_start: 0.8974 (mmm) cc_final: 0.8606 (mmm) REVERT: C 813 GLU cc_start: 0.8960 (pp20) cc_final: 0.8622 (tt0) REVERT: C 815 CYS cc_start: 0.7711 (m) cc_final: 0.6527 (p) REVERT: C 852 LEU cc_start: 0.7784 (tp) cc_final: 0.7546 (tp) REVERT: C 874 GLN cc_start: 0.7249 (pt0) cc_final: 0.5515 (mm110) REVERT: C 937 PHE cc_start: 0.8323 (t80) cc_final: 0.8106 (t80) REVERT: C 938 PHE cc_start: 0.7728 (m-10) cc_final: 0.7468 (m-80) REVERT: C 955 ARG cc_start: 0.5058 (mmm-85) cc_final: 0.3406 (ptt90) REVERT: C 1023 MET cc_start: 0.8543 (mtp) cc_final: 0.8088 (mtp) REVERT: D 585 MET cc_start: 0.8764 (mmm) cc_final: 0.8303 (ttm) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.2418 time to fit residues: 136.2313 Evaluate side-chains 268 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 1.9990 chunk 170 optimal weight: 0.0770 chunk 49 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN B 461 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094262 restraints weight = 44972.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096743 restraints weight = 28439.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.098416 restraints weight = 19750.504| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17048 Z= 0.213 Angle : 0.661 13.752 22878 Z= 0.335 Chirality : 0.043 0.284 2494 Planarity : 0.005 0.079 2774 Dihedral : 14.981 178.931 2782 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 2020 helix: 1.25 (0.16), residues: 1076 sheet: -2.11 (0.34), residues: 190 loop : -1.65 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 460 HIS 0.008 0.001 HIS C 883 PHE 0.054 0.002 PHE A 938 TYR 0.020 0.001 TYR C1026 ARG 0.004 0.000 ARG C 897 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3662.64 seconds wall clock time: 67 minutes 2.32 seconds (4022.32 seconds total)