Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 05:03:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/04_2023/7rz8_24754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/04_2023/7rz8_24754.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/04_2023/7rz8_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_24754/04_2023/7rz8_24754_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/04_2023/7rz8_24754_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/04_2023/7rz8_24754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/04_2023/7rz8_24754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/04_2023/7rz8_24754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz8_24754/04_2023/7rz8_24754_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 127 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: 54 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: 127 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: 54 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: 9.02, per 1000 atoms: 0.54 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: 6.98 Conformation dependent library (CDL) restraints added in 2.5 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: 1.78 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: 4.78 Time building geometry restraints manager: 7.38 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: 9776 35.75 - 71.50: 266 71.50 - 107.25: 22 107.25 - 143.00: 6 143.00 - 178.75: 8 Dihedral angle restraints: 10078 sinusoidal: 4212 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 10075 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.940 Check model and map are aligned: 0.270 Set scattering table: 0.210 Process input model: 43.910 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.630 ------------------------------------------------------------------------------- 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 : 16.281 178.748 6320 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 % 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 *********************** 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 : 1.990 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 outliers start: 16 outliers final: 6 residues processed: 632 average time/residue: 0.2908 time to fit residues: 271.0892 Evaluate side-chains 343 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 337 time to evaluate : 1.969 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2552 time to fit residues: 4.9277 ------------------------------------------------------------------------------- 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: 1.9990 chunk 52 optimal weight: 0.0010 chunk 103 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 569 ASN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 17048 Z= 0.178 Angle : 0.628 8.644 22878 Z= 0.331 Chirality : 0.043 0.221 2494 Planarity : 0.006 0.076 2774 Dihedral : 17.443 179.855 2634 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.23 % 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: -0.16 (0.14), residues: 1100 sheet: -2.00 (0.33), residues: 204 loop : -2.05 (0.22), residues: 716 *********************** 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 478 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 474 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 477 average time/residue: 0.2707 time to fit residues: 199.3800 Evaluate side-chains 302 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6125 ------------------------------------------------------------------------------- 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: 10.0000 chunk 152 optimal weight: 1.9990 chunk 124 optimal weight: 0.0670 chunk 50 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- 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 726 ASN A 947 ASN B 586 GLN ** B 619 ASN ** 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 726 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 17048 Z= 0.353 Angle : 0.718 9.358 22878 Z= 0.378 Chirality : 0.045 0.209 2494 Planarity : 0.005 0.075 2774 Dihedral : 17.054 174.166 2634 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.29 % 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: -0.85 (0.18), residues: 2020 helix: 0.61 (0.15), residues: 1078 sheet: -2.18 (0.35), residues: 176 loop : -1.84 (0.22), residues: 766 *********************** 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 399 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 394 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 397 average time/residue: 0.2643 time to fit residues: 164.0845 Evaluate side-chains 278 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7691 ------------------------------------------------------------------------------- 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: 0.7980 chunk 138 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 435 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** 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** C 947 ASN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 17048 Z= 0.242 Angle : 0.660 22.476 22878 Z= 0.346 Chirality : 0.045 0.410 2494 Planarity : 0.005 0.074 2774 Dihedral : 16.297 170.890 2634 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.11 % 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: -0.59 (0.19), residues: 2020 helix: 0.93 (0.16), residues: 1070 sheet: -1.94 (0.34), residues: 186 loop : -1.89 (0.22), residues: 764 *********************** 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 373 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 369 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 372 average time/residue: 0.2517 time to fit residues: 147.6803 Evaluate side-chains 278 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6917 ------------------------------------------------------------------------------- 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: 0.9980 chunk 110 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** 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** ** 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: 0.7650 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 17048 Z= 0.197 Angle : 0.640 23.023 22878 Z= 0.329 Chirality : 0.044 0.408 2494 Planarity : 0.005 0.076 2774 Dihedral : 15.536 171.819 2634 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.05 % 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: 1.14 (0.16), residues: 1064 sheet: -1.82 (0.33), residues: 202 loop : -1.77 (0.22), residues: 754 *********************** 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 378 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 374 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 378 average time/residue: 0.2506 time to fit residues: 149.4206 Evaluate side-chains 267 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.842 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6205 ------------------------------------------------------------------------------- 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: 5.9990 chunk 175 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 114 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 17048 Z= 0.221 Angle : 0.644 18.577 22878 Z= 0.330 Chirality : 0.043 0.318 2494 Planarity : 0.005 0.076 2774 Dihedral : 15.154 169.647 2634 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 0.06 % 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: -0.30 (0.19), residues: 2020 helix: 1.17 (0.16), residues: 1062 sheet: -1.94 (0.34), residues: 184 loop : -1.71 (0.22), residues: 774 *********************** 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 356 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 356 average time/residue: 0.2510 time to fit residues: 141.8155 Evaluate side-chains 264 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6138 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN 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** ** D 587 GLN ** 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: 0.7626 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 17048 Z= 0.174 Angle : 0.624 17.973 22878 Z= 0.319 Chirality : 0.043 0.379 2494 Planarity : 0.005 0.078 2774 Dihedral : 14.564 166.783 2634 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.00 % 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: -0.27 (0.19), residues: 2020 helix: 1.17 (0.16), residues: 1072 sheet: -1.86 (0.34), residues: 182 loop : -1.71 (0.22), residues: 766 *********************** 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 359 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.2451 time to fit residues: 140.7716 Evaluate side-chains 266 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.919 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3079 ------------------------------------------------------------------------------- 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: 0.9990 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 418 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 764 ASN C 435 HIS ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5778 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= 0.192 Angle : 0.635 14.713 22878 Z= 0.324 Chirality : 0.043 0.337 2494 Planarity : 0.005 0.079 2774 Dihedral : 14.267 158.679 2634 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % 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: -0.29 (0.19), residues: 2020 helix: 1.16 (0.16), residues: 1072 sheet: -1.87 (0.32), residues: 202 loop : -1.71 (0.23), residues: 746 *********************** 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 351 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 350 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 350 average time/residue: 0.2541 time to fit residues: 141.5886 Evaluate side-chains 263 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5436 ------------------------------------------------------------------------------- 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: 8.9990 chunk 181 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 142 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** B 461 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 17048 Z= 0.199 Angle : 0.639 15.632 22878 Z= 0.327 Chirality : 0.043 0.321 2494 Planarity : 0.005 0.080 2774 Dihedral : 14.063 152.363 2634 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % 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: -0.25 (0.19), residues: 2020 helix: 1.17 (0.16), residues: 1072 sheet: -1.69 (0.35), residues: 182 loop : -1.72 (0.22), residues: 766 *********************** 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 338 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2514 time to fit residues: 135.7816 Evaluate side-chains 262 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6240 ------------------------------------------------------------------------------- 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: 0.5980 chunk 191 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 133 optimal weight: 0.6980 chunk 201 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 586 GLN A 587 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 764 ASN C 435 HIS ** 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 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 17048 Z= 0.197 Angle : 0.650 14.749 22878 Z= 0.330 Chirality : 0.043 0.276 2494 Planarity : 0.005 0.084 2774 Dihedral : 13.847 152.970 2634 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.00 % 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: -0.23 (0.19), residues: 2020 helix: 1.20 (0.16), residues: 1066 sheet: -1.83 (0.36), residues: 180 loop : -1.67 (0.22), residues: 774 ********************** 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 350 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.2507 time to fit residues: 140.9157 Evaluate side-chains 268 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5942 ------------------------------------------------------------------------------- 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: 5.9990 chunk 170 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 147 optimal weight: 0.3980 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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** B 461 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 764 ASN C 435 HIS C 508 GLN C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 GLN C 947 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.119362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093038 restraints weight = 45006.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095331 restraints weight = 29722.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096576 restraints weight = 19590.176| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 17048 Z= 0.294 Angle : 0.701 14.114 22878 Z= 0.361 Chirality : 0.045 0.294 2494 Planarity : 0.005 0.080 2774 Dihedral : 14.223 154.189 2634 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.00 % 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: -0.31 (0.19), residues: 2020 helix: 1.16 (0.16), residues: 1052 sheet: -1.89 (0.33), residues: 202 loop : -1.65 (0.22), residues: 766 =============================================================================== Job complete usr+sys time: 3538.16 seconds wall clock time: 65 minutes 16.73 seconds (3916.73 seconds total)