Starting phenix.real_space_refine on Fri Feb 16 16:19:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/02_2024/7ryy_24748_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/02_2024/7ryy_24748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/02_2024/7ryy_24748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/02_2024/7ryy_24748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/02_2024/7ryy_24748_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/02_2024/7ryy_24748_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 106 5.16 5 C 10288 2.51 5 N 2538 2.21 5 O 2902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 899": "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 "C ARG 453": "NH1" <-> "NH2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 899": "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" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15836 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4698 Classifications: {'peptide': 602} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 585} Chain breaks: 4 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3177 Classifications: {'peptide': 408} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 394} Chain breaks: 1 Chain: "C" Number of atoms: 4698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4698 Classifications: {'peptide': 602} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 585} Chain breaks: 4 Chain: "D" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3177 Classifications: {'peptide': 408} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 394} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'PCW': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'PCW': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 9.07, per 1000 atoms: 0.57 Number of scatterers: 15836 At special positions: 0 Unit cell: (120.512, 133.424, 129.12, 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 2 15.00 O 2902 8.00 N 2538 7.00 C 10288 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=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.48 Conformation dependent library (CDL) restraints added in 3.0 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 16 sheets defined 51.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 516 through 520 Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.761A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 629 removed outlier: 3.711A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (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: 3.721A 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 756 removed outlier: 3.562A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 768 removed outlier: 4.153A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 821 removed outlier: 3.539A pdb=" N LEU A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 857 removed outlier: 4.165A pdb=" N ALA A 836 " --> pdb=" O CYS A 832 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 950 removed outlier: 3.780A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA A 928 " --> pdb=" O MET A 924 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 929 " --> pdb=" O ILE A 925 " (cutoff:3.500A) Proline residue: A 930 - end of helix removed outlier: 3.851A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 990 removed outlier: 3.687A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 964 " --> pdb=" O PHE A 960 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 984 " --> pdb=" O TYR A 980 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1034 removed outlier: 3.641A pdb=" N LEU A1016 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 464 through 468 Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.836A 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 545 removed outlier: 3.776A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.782A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 625 removed outlier: 3.825A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.551A 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: 3.513A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 696 removed outlier: 3.500A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 743 through 756 removed outlier: 4.296A pdb=" N GLN B 756 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 removed outlier: 3.691A pdb=" N LYS B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 780 removed outlier: 4.390A pdb=" N SER B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 776 through 780' Processing helix chain 'B' and resid 793 through 820 removed outlier: 3.639A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 816 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA B 820 " --> 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 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 520 Proline residue: C 520 - end of helix Processing helix chain 'C' and resid 523 through 544 removed outlier: 3.762A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 629 removed outlier: 3.711A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (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: 3.720A 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 756 removed outlier: 3.563A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 768 removed outlier: 4.153A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 821 removed outlier: 3.538A pdb=" N LEU C 805 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 857 removed outlier: 4.163A pdb=" N ALA C 836 " --> pdb=" O CYS C 832 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 950 removed outlier: 3.780A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA C 928 " --> pdb=" O MET C 924 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR C 929 " --> pdb=" O ILE C 925 " (cutoff:3.500A) Proline residue: C 930 - end of helix removed outlier: 3.851A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 938 " --> pdb=" O VAL C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 990 removed outlier: 3.687A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 964 " --> pdb=" O PHE C 960 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 984 " --> pdb=" O TYR C 980 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 989 " --> pdb=" O ASN C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1034 removed outlier: 3.641A pdb=" N LEU C1016 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR C1017 " --> pdb=" O SER C1013 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C1022 " --> pdb=" O GLU C1018 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 483 through 488 removed outlier: 3.836A 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 545 removed outlier: 3.776A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.782A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 removed outlier: 3.823A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.549A 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: 3.512A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 696 removed outlier: 3.501A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 743 through 756 removed outlier: 4.296A pdb=" N GLN D 756 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 removed outlier: 3.691A pdb=" N LYS D 763 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 780 removed outlier: 4.389A pdb=" N SER D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 776 through 780' Processing helix chain 'D' and resid 793 through 820 removed outlier: 3.639A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA D 820 " --> 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: 4.015A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 732 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 3.717A 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: 3.572A pdb=" N MET A 721 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 997 through 1003 removed outlier: 3.557A pdb=" N GLY A 867 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A1002 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 884 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 868 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A 878 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS A 883 " --> pdb=" O CYS A 890 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 890 " --> pdb=" O HIS A 883 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 397 through 399 removed outlier: 3.986A pdb=" N THR B 399 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= H, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.355A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= J, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= K, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.015A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 732 " --> pdb=" O MET C 496 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 720 through 723 removed outlier: 3.572A pdb=" N MET C 721 " --> pdb=" O ILE C 504 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 997 through 1003 removed outlier: 3.556A pdb=" N GLY C 867 " --> pdb=" O TYR C 998 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C1002 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 884 " --> pdb=" O LEU C 862 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE C 868 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL C 878 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS C 883 " --> pdb=" O CYS C 890 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS C 890 " --> pdb=" O HIS C 883 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 397 through 399 removed outlier: 3.988A pdb=" N THR D 399 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= P, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.355A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2124 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: 4.58 Time building geometry restraints manager: 6.95 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: 2516 1.31 - 1.44: 4378 1.44 - 1.57: 9092 1.57 - 1.69: 6 1.69 - 1.82: 176 Bond restraints: 16168 Sorted by residual: bond pdb=" C31 PCW C1101 " pdb=" O2 PCW C1101 " ideal model delta sigma weight residual 1.333 1.428 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C31 PCW A1101 " pdb=" O2 PCW A1101 " ideal model delta sigma weight residual 1.333 1.427 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C31 PCW C1101 " pdb=" C32 PCW C1101 " ideal model delta sigma weight residual 1.502 1.554 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C31 PCW A1101 " pdb=" C32 PCW A1101 " ideal model delta sigma weight residual 1.502 1.554 -0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" C36 PCW A1101 " pdb=" C37 PCW A1101 " ideal model delta sigma weight residual 1.524 1.573 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 16163 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.99: 298 105.99 - 113.22: 8716 113.22 - 120.46: 6353 120.46 - 127.70: 6316 127.70 - 134.93: 133 Bond angle restraints: 21816 Sorted by residual: angle pdb=" C LYS C 716 " pdb=" N PRO C 717 " pdb=" CA PRO C 717 " ideal model delta sigma weight residual 119.84 112.01 7.83 1.25e+00 6.40e-01 3.93e+01 angle pdb=" C LYS A 716 " pdb=" N PRO A 717 " pdb=" CA PRO A 717 " ideal model delta sigma weight residual 119.84 112.02 7.82 1.25e+00 6.40e-01 3.91e+01 angle pdb=" C SER C 635 " pdb=" N ALA C 636 " pdb=" CA ALA C 636 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C SER A 635 " pdb=" N ALA A 636 " pdb=" CA ALA A 636 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" CA LEU C 882 " pdb=" CB LEU C 882 " pdb=" CG LEU C 882 " ideal model delta sigma weight residual 116.30 130.59 -14.29 3.50e+00 8.16e-02 1.67e+01 ... (remaining 21811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 8814 15.16 - 30.32: 538 30.32 - 45.48: 191 45.48 - 60.64: 21 60.64 - 75.81: 10 Dihedral angle restraints: 9574 sinusoidal: 3778 harmonic: 5796 Sorted by residual: dihedral pdb=" CA LYS D 716 " pdb=" C LYS D 716 " pdb=" N PRO D 717 " pdb=" CA PRO D 717 " ideal model delta harmonic sigma weight residual 180.00 140.51 39.49 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA LYS B 716 " pdb=" C LYS B 716 " pdb=" N PRO B 717 " pdb=" CA PRO B 717 " ideal model delta harmonic sigma weight residual 180.00 140.52 39.48 0 5.00e+00 4.00e-02 6.24e+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 93.00 161.74 -68.74 1 1.00e+01 1.00e-02 6.12e+01 ... (remaining 9571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1859 0.054 - 0.107: 476 0.107 - 0.161: 90 0.161 - 0.214: 21 0.214 - 0.268: 8 Chirality restraints: 2454 Sorted by residual: chirality pdb=" CG LEU A 882 " pdb=" CB LEU A 882 " pdb=" CD1 LEU A 882 " pdb=" CD2 LEU A 882 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU C 882 " pdb=" CB LEU C 882 " pdb=" CD1 LEU C 882 " pdb=" CD2 LEU C 882 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CG LEU C 989 " pdb=" CB LEU C 989 " pdb=" CD1 LEU C 989 " pdb=" CD2 LEU C 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2451 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 716 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 717 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO C 717 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO B 717 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " 0.057 5.00e-02 4.00e+02 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2997 2.76 - 3.30: 15312 3.30 - 3.83: 26318 3.83 - 4.37: 30953 4.37 - 4.90: 50596 Nonbonded interactions: 126176 Sorted by model distance: nonbonded pdb=" O LEU D 639 " pdb=" OH TYR D 647 " model vdw 2.230 2.440 nonbonded pdb=" O LEU B 639 " pdb=" OH TYR B 647 " model vdw 2.230 2.440 nonbonded pdb=" OG SER D 706 " pdb=" OD1 ASN D 726 " model vdw 2.278 2.440 nonbonded pdb=" OG SER B 706 " pdb=" OD1 ASN B 726 " model vdw 2.278 2.440 nonbonded pdb=" O PHE C 943 " pdb=" OG SER C 946 " model vdw 2.321 2.440 ... (remaining 126171 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' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 10.850 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 44.430 Find NCS groups from input model: 0.840 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5203 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 : 0.005 0.095 16168 Z= 0.342 Angle : 1.006 14.292 21816 Z= 0.550 Chirality : 0.052 0.268 2454 Planarity : 0.007 0.104 2684 Dihedral : 11.501 75.805 5856 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.59 % Allowed : 5.74 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % 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: -4.08 (0.14), residues: 1992 helix: -2.72 (0.10), residues: 1048 sheet: -2.53 (0.33), residues: 156 loop : -2.46 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 767 HIS 0.004 0.001 HIS D 435 PHE 0.019 0.002 PHE C 901 TYR 0.018 0.002 TYR C 647 ARG 0.006 0.001 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 465 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 PHE cc_start: 0.7408 (m-10) cc_final: 0.6976 (m-80) REVERT: A 684 ARG cc_start: 0.7965 (mpp-170) cc_final: 0.7309 (tmt-80) REVERT: A 704 LEU cc_start: 0.7584 (pt) cc_final: 0.7083 (pt) REVERT: A 708 MET cc_start: 0.8204 (mtt) cc_final: 0.7428 (ptm) REVERT: A 712 ILE cc_start: 0.8670 (mm) cc_final: 0.8073 (mm) REVERT: A 721 MET cc_start: 0.3323 (ptm) cc_final: 0.2641 (ppp) REVERT: A 860 TYR cc_start: 0.3924 (m-80) cc_final: 0.3608 (m-80) REVERT: B 519 ASP cc_start: 0.8301 (t0) cc_final: 0.8021 (t0) REVERT: B 579 PHE cc_start: 0.4285 (t80) cc_final: 0.3702 (t80) REVERT: B 593 PRO cc_start: 0.7307 (Cg_exo) cc_final: 0.6683 (Cg_endo) REVERT: B 699 LYS cc_start: 0.8576 (mptt) cc_final: 0.7978 (mmmt) REVERT: B 708 MET cc_start: 0.8146 (mtt) cc_final: 0.7457 (tpt) REVERT: C 402 GLU cc_start: 0.7329 (tp30) cc_final: 0.7022 (tp30) REVERT: C 424 TYR cc_start: 0.7162 (t80) cc_final: 0.6601 (t80) REVERT: C 457 THR cc_start: 0.7661 (p) cc_final: 0.7451 (p) REVERT: C 479 LEU cc_start: 0.8689 (tp) cc_final: 0.8390 (tp) REVERT: C 519 ASP cc_start: 0.6552 (m-30) cc_final: 0.5893 (t0) REVERT: C 521 LEU cc_start: 0.6881 (mt) cc_final: 0.6569 (mt) REVERT: C 672 THR cc_start: 0.7772 (m) cc_final: 0.7570 (p) REVERT: C 710 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8569 (tp30) REVERT: C 713 GLU cc_start: 0.9093 (tt0) cc_final: 0.8865 (mt-10) REVERT: C 720 THR cc_start: 0.8104 (p) cc_final: 0.7598 (t) REVERT: C 732 TYR cc_start: 0.3989 (m-10) cc_final: 0.3700 (m-10) REVERT: C 762 LEU cc_start: 0.9086 (mt) cc_final: 0.8673 (mm) REVERT: C 796 PHE cc_start: 0.7147 (m-80) cc_final: 0.6712 (m-80) REVERT: C 880 MET cc_start: 0.5000 (tmm) cc_final: 0.4424 (ttt) REVERT: C 1003 TYR cc_start: 0.5709 (m-80) cc_final: 0.5490 (m-80) REVERT: D 407 MET cc_start: 0.3927 (mtm) cc_final: 0.2923 (mmp) REVERT: D 463 MET cc_start: 0.7744 (mtm) cc_final: 0.7325 (mtm) REVERT: D 527 MET cc_start: 0.5979 (ttm) cc_final: 0.5643 (ttm) REVERT: D 629 MET cc_start: 0.6645 (mmm) cc_final: 0.4964 (tpp) REVERT: D 649 THR cc_start: 0.2950 (p) cc_final: 0.2688 (p) REVERT: D 760 ASP cc_start: 0.7170 (m-30) cc_final: 0.6946 (t0) REVERT: D 763 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8747 (tptt) outliers start: 10 outliers final: 2 residues processed: 472 average time/residue: 0.3179 time to fit residues: 211.1533 Evaluate side-chains 279 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.0370 chunk 151 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 575 ASN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 874 GLN A 950 HIS ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 569 ASN B 586 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN B 764 ASN C 575 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN C 985 ASN D 418 ASN D 461 ASN D 587 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5726 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16168 Z= 0.208 Angle : 0.663 10.993 21816 Z= 0.345 Chirality : 0.043 0.332 2454 Planarity : 0.006 0.084 2684 Dihedral : 7.062 59.185 2208 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.29 % Allowed : 4.69 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 1992 helix: -0.01 (0.14), residues: 1078 sheet: -1.74 (0.32), residues: 206 loop : -1.96 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 767 HIS 0.003 0.001 HIS C 883 PHE 0.027 0.002 PHE A 901 TYR 0.020 0.002 TYR A1003 ARG 0.012 0.001 ARG C 675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 337 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.8009 (tpp) cc_final: 0.7776 (tpp) REVERT: A 591 ILE cc_start: 0.5282 (tp) cc_final: 0.4862 (tp) REVERT: A 684 ARG cc_start: 0.7873 (mpp-170) cc_final: 0.7167 (tmt-80) REVERT: A 704 LEU cc_start: 0.7533 (pt) cc_final: 0.6281 (pt) REVERT: A 707 THR cc_start: 0.7890 (m) cc_final: 0.7650 (p) REVERT: A 708 MET cc_start: 0.8312 (mtt) cc_final: 0.7560 (ptm) REVERT: A 709 ASN cc_start: 0.6822 (t0) cc_final: 0.6386 (t0) REVERT: A 721 MET cc_start: 0.2687 (ptm) cc_final: 0.0668 (ppp) REVERT: A 860 TYR cc_start: 0.4209 (m-80) cc_final: 0.3585 (m-80) REVERT: A 939 MET cc_start: 0.4976 (ttt) cc_final: 0.4417 (ttt) REVERT: A 941 ILE cc_start: 0.7559 (mt) cc_final: 0.7310 (mt) REVERT: B 519 ASP cc_start: 0.8539 (t0) cc_final: 0.8236 (t0) REVERT: B 596 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7639 (pp) REVERT: B 661 ARG cc_start: 0.8600 (tpm170) cc_final: 0.8198 (tpp80) REVERT: B 699 LYS cc_start: 0.8835 (mptt) cc_final: 0.8586 (mmmt) REVERT: B 708 MET cc_start: 0.8177 (mtt) cc_final: 0.7424 (tpt) REVERT: C 414 MET cc_start: 0.5625 (mpp) cc_final: 0.5229 (mpp) REVERT: C 424 TYR cc_start: 0.7548 (t80) cc_final: 0.6819 (t80) REVERT: C 519 ASP cc_start: 0.7088 (m-30) cc_final: 0.6712 (t70) REVERT: C 527 MET cc_start: 0.8531 (mtm) cc_final: 0.7040 (mtp) REVERT: C 658 PHE cc_start: 0.8233 (t80) cc_final: 0.7718 (t80) REVERT: C 710 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8578 (mm-30) REVERT: C 714 GLN cc_start: 0.8048 (mp-120) cc_final: 0.7779 (pt0) REVERT: C 762 LEU cc_start: 0.9122 (mt) cc_final: 0.8396 (mt) REVERT: C 796 PHE cc_start: 0.7502 (m-80) cc_final: 0.7121 (m-80) REVERT: C 980 TYR cc_start: 0.7289 (t80) cc_final: 0.6756 (t80) REVERT: C 1003 TYR cc_start: 0.5942 (m-80) cc_final: 0.4964 (m-80) REVERT: C 1032 TYR cc_start: 0.8392 (t80) cc_final: 0.8109 (t80) REVERT: D 405 TYR cc_start: 0.8085 (m-80) cc_final: 0.7718 (m-80) REVERT: D 407 MET cc_start: 0.4857 (mtm) cc_final: 0.4171 (mmp) REVERT: D 463 MET cc_start: 0.7953 (mtm) cc_final: 0.7642 (mtm) REVERT: D 527 MET cc_start: 0.6010 (ttm) cc_final: 0.5602 (ttm) REVERT: D 629 MET cc_start: 0.6809 (mmm) cc_final: 0.5168 (tpp) REVERT: D 760 ASP cc_start: 0.7213 (m-30) cc_final: 0.6804 (t0) REVERT: D 763 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8803 (tptt) REVERT: D 790 SER cc_start: 0.7560 (m) cc_final: 0.7312 (p) outliers start: 5 outliers final: 1 residues processed: 342 average time/residue: 0.2918 time to fit residues: 144.2901 Evaluate side-chains 247 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 245 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 123 optimal weight: 0.0030 chunk 50 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5964 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 16168 Z= 0.191 Angle : 0.634 10.981 21816 Z= 0.326 Chirality : 0.042 0.483 2454 Planarity : 0.005 0.071 2684 Dihedral : 6.542 56.159 2208 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.12 % Allowed : 3.28 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 1992 helix: 0.88 (0.15), residues: 1090 sheet: -1.06 (0.35), residues: 202 loop : -1.65 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 861 HIS 0.003 0.001 HIS B 412 PHE 0.021 0.001 PHE A 965 TYR 0.041 0.002 TYR A 980 ARG 0.006 0.001 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 340 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.6298 (mmt) cc_final: 0.5862 (tpp) REVERT: A 585 MET cc_start: 0.8268 (tpp) cc_final: 0.7926 (tpp) REVERT: A 591 ILE cc_start: 0.6073 (tp) cc_final: 0.5755 (tp) REVERT: A 684 ARG cc_start: 0.7979 (mpp-170) cc_final: 0.7077 (tmt-80) REVERT: A 704 LEU cc_start: 0.7693 (pt) cc_final: 0.4591 (pt) REVERT: A 707 THR cc_start: 0.8039 (m) cc_final: 0.7781 (p) REVERT: A 708 MET cc_start: 0.8575 (mtt) cc_final: 0.8019 (ptm) REVERT: A 939 MET cc_start: 0.5271 (ttt) cc_final: 0.4719 (ttt) REVERT: B 460 TRP cc_start: 0.7041 (m100) cc_final: 0.6418 (m-90) REVERT: B 531 PHE cc_start: 0.8179 (t80) cc_final: 0.7942 (t80) REVERT: B 619 ASN cc_start: 0.6208 (t0) cc_final: 0.4179 (t0) REVERT: B 620 LEU cc_start: 0.8758 (tt) cc_final: 0.8534 (tt) REVERT: B 623 PHE cc_start: 0.7880 (m-10) cc_final: 0.7530 (m-10) REVERT: B 661 ARG cc_start: 0.8631 (tpm170) cc_final: 0.8242 (tpp80) REVERT: B 708 MET cc_start: 0.8167 (mtt) cc_final: 0.7460 (tpt) REVERT: C 414 MET cc_start: 0.6044 (mpp) cc_final: 0.5741 (mpp) REVERT: C 424 TYR cc_start: 0.7719 (t80) cc_final: 0.7104 (t80) REVERT: C 637 GLU cc_start: 0.8441 (mp0) cc_final: 0.8042 (mp0) REVERT: C 664 ILE cc_start: 0.7182 (mp) cc_final: 0.6965 (mp) REVERT: C 710 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8600 (mm-30) REVERT: C 762 LEU cc_start: 0.9211 (mt) cc_final: 0.8543 (mp) REVERT: C 811 LEU cc_start: 0.9588 (tp) cc_final: 0.9289 (mt) REVERT: C 840 LEU cc_start: 0.8903 (mt) cc_final: 0.8585 (mt) REVERT: C 1032 TYR cc_start: 0.8347 (t80) cc_final: 0.8083 (t80) REVERT: D 405 TYR cc_start: 0.8070 (m-80) cc_final: 0.7858 (m-80) REVERT: D 407 MET cc_start: 0.5009 (mtm) cc_final: 0.4394 (mmp) REVERT: D 458 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8380 (mmmt) REVERT: D 463 MET cc_start: 0.7953 (mtm) cc_final: 0.7661 (mtp) REVERT: D 496 MET cc_start: 0.4638 (pmm) cc_final: 0.4225 (pmm) REVERT: D 503 MET cc_start: 0.7747 (ppp) cc_final: 0.7230 (ppp) REVERT: D 527 MET cc_start: 0.6260 (ttm) cc_final: 0.5760 (ttm) REVERT: D 647 TYR cc_start: 0.6849 (m-80) cc_final: 0.6097 (m-80) REVERT: D 760 ASP cc_start: 0.7137 (m-30) cc_final: 0.6832 (t0) outliers start: 2 outliers final: 1 residues processed: 342 average time/residue: 0.2744 time to fit residues: 137.5625 Evaluate side-chains 259 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 3.9990 chunk 136 optimal weight: 0.0000 chunk 94 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 0.0370 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 95 optimal weight: 0.0970 chunk 173 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.6264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN D 418 ASN D 586 GLN D 587 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16168 Z= 0.164 Angle : 0.582 11.008 21816 Z= 0.298 Chirality : 0.041 0.218 2454 Planarity : 0.005 0.070 2684 Dihedral : 6.262 59.270 2208 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1992 helix: 1.43 (0.16), residues: 1066 sheet: -1.17 (0.38), residues: 164 loop : -1.50 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 526 HIS 0.003 0.001 HIS A 950 PHE 0.031 0.001 PHE C 844 TYR 0.013 0.001 TYR A 702 ARG 0.016 0.001 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 328 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.6233 (mmt) cc_final: 0.5715 (tpp) REVERT: A 571 PHE cc_start: 0.7557 (m-10) cc_final: 0.7295 (m-10) REVERT: A 585 MET cc_start: 0.8100 (tpp) cc_final: 0.7707 (tpp) REVERT: A 629 MET cc_start: 0.8010 (mmt) cc_final: 0.7804 (mmt) REVERT: A 704 LEU cc_start: 0.7560 (pt) cc_final: 0.6350 (pt) REVERT: A 707 THR cc_start: 0.8184 (m) cc_final: 0.7971 (p) REVERT: A 708 MET cc_start: 0.8495 (mtt) cc_final: 0.8190 (ptm) REVERT: A 721 MET cc_start: 0.2979 (ppp) cc_final: 0.2121 (ppp) REVERT: A 939 MET cc_start: 0.5318 (ttt) cc_final: 0.4694 (ttt) REVERT: B 460 TRP cc_start: 0.6932 (m100) cc_final: 0.6349 (m-90) REVERT: B 519 ASP cc_start: 0.8677 (t0) cc_final: 0.8451 (t0) REVERT: B 520 PRO cc_start: 0.8083 (Cg_endo) cc_final: 0.7468 (Cg_exo) REVERT: B 531 PHE cc_start: 0.8165 (t80) cc_final: 0.7945 (t80) REVERT: B 620 LEU cc_start: 0.8851 (tt) cc_final: 0.8481 (tt) REVERT: B 627 GLU cc_start: 0.6463 (pm20) cc_final: 0.6087 (tp30) REVERT: B 661 ARG cc_start: 0.8647 (tpm170) cc_final: 0.8254 (tpp80) REVERT: B 708 MET cc_start: 0.8271 (mtt) cc_final: 0.7464 (tpt) REVERT: C 414 MET cc_start: 0.6165 (mpp) cc_final: 0.5909 (mpp) REVERT: C 424 TYR cc_start: 0.7761 (t80) cc_final: 0.7193 (t80) REVERT: C 637 GLU cc_start: 0.8317 (mp0) cc_final: 0.8062 (mp0) REVERT: C 668 ASP cc_start: 0.8717 (m-30) cc_final: 0.8330 (m-30) REVERT: C 713 GLU cc_start: 0.8870 (pt0) cc_final: 0.8575 (pt0) REVERT: C 762 LEU cc_start: 0.9336 (mt) cc_final: 0.8677 (mp) REVERT: C 796 PHE cc_start: 0.8505 (m-80) cc_final: 0.8288 (m-80) REVERT: C 811 LEU cc_start: 0.9595 (tp) cc_final: 0.9281 (mt) REVERT: C 840 LEU cc_start: 0.9038 (mt) cc_final: 0.8785 (mt) REVERT: C 1032 TYR cc_start: 0.8332 (t80) cc_final: 0.8051 (t80) REVERT: D 407 MET cc_start: 0.5047 (mtm) cc_final: 0.4553 (mmp) REVERT: D 414 MET cc_start: 0.5585 (mpp) cc_final: 0.5365 (mpp) REVERT: D 458 LYS cc_start: 0.8812 (mmtp) cc_final: 0.8476 (mmmt) REVERT: D 463 MET cc_start: 0.7943 (mtm) cc_final: 0.7665 (mmm) REVERT: D 527 MET cc_start: 0.6467 (ttm) cc_final: 0.5955 (ttm) REVERT: D 649 THR cc_start: 0.4031 (p) cc_final: 0.3664 (p) REVERT: D 670 MET cc_start: 0.7691 (ppp) cc_final: 0.7368 (tmm) REVERT: D 674 MET cc_start: 0.8313 (mmp) cc_final: 0.7948 (mmm) REVERT: D 760 ASP cc_start: 0.7270 (m-30) cc_final: 0.6793 (t0) outliers start: 1 outliers final: 0 residues processed: 329 average time/residue: 0.2783 time to fit residues: 135.0427 Evaluate side-chains 261 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 143 optimal weight: 0.0970 chunk 79 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN ** 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: 0.6264 moved from start: 0.7717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16168 Z= 0.158 Angle : 0.587 10.118 21816 Z= 0.300 Chirality : 0.040 0.192 2454 Planarity : 0.005 0.065 2684 Dihedral : 6.069 59.609 2208 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 1992 helix: 1.49 (0.16), residues: 1096 sheet: -1.21 (0.35), residues: 186 loop : -1.39 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 767 HIS 0.002 0.001 HIS D 435 PHE 0.022 0.001 PHE A 965 TYR 0.020 0.001 TYR D 424 ARG 0.005 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.6523 (mmt) cc_final: 0.5962 (tpp) REVERT: A 585 MET cc_start: 0.7877 (tpp) cc_final: 0.7465 (tpp) REVERT: A 704 LEU cc_start: 0.7868 (pt) cc_final: 0.6835 (pt) REVERT: A 707 THR cc_start: 0.8315 (m) cc_final: 0.8111 (p) REVERT: A 708 MET cc_start: 0.8550 (mtt) cc_final: 0.8347 (ptm) REVERT: A 721 MET cc_start: 0.2979 (ppp) cc_final: 0.2720 (ppp) REVERT: A 753 LEU cc_start: 0.6738 (mp) cc_final: 0.6511 (mt) REVERT: A 939 MET cc_start: 0.5625 (ttt) cc_final: 0.4199 (tmm) REVERT: A 988 MET cc_start: 0.2850 (tpt) cc_final: 0.2599 (tpt) REVERT: B 460 TRP cc_start: 0.6866 (m100) cc_final: 0.6282 (m-90) REVERT: B 587 GLN cc_start: 0.6417 (mm110) cc_final: 0.5959 (mm110) REVERT: B 708 MET cc_start: 0.8149 (mtt) cc_final: 0.7494 (tpt) REVERT: B 789 LEU cc_start: 0.7392 (tp) cc_final: 0.6744 (pt) REVERT: B 797 TYR cc_start: 0.7145 (m-80) cc_final: 0.6812 (m-10) REVERT: C 424 TYR cc_start: 0.8111 (t80) cc_final: 0.7562 (t80) REVERT: C 500 ILE cc_start: 0.7480 (mt) cc_final: 0.7002 (mt) REVERT: C 531 PHE cc_start: 0.8668 (m-10) cc_final: 0.8440 (m-80) REVERT: C 586 GLN cc_start: 0.5236 (tm-30) cc_final: 0.4744 (tm-30) REVERT: C 637 GLU cc_start: 0.8340 (mp0) cc_final: 0.7883 (mp0) REVERT: C 664 ILE cc_start: 0.6911 (mp) cc_final: 0.6612 (mp) REVERT: C 668 ASP cc_start: 0.8766 (m-30) cc_final: 0.8441 (m-30) REVERT: C 713 GLU cc_start: 0.8859 (pt0) cc_final: 0.8630 (pt0) REVERT: C 762 LEU cc_start: 0.9301 (mt) cc_final: 0.8659 (mp) REVERT: C 796 PHE cc_start: 0.8720 (m-80) cc_final: 0.8431 (m-80) REVERT: C 811 LEU cc_start: 0.9621 (tp) cc_final: 0.9273 (mt) REVERT: C 840 LEU cc_start: 0.8984 (mt) cc_final: 0.8683 (mt) REVERT: C 999 PHE cc_start: 0.8235 (t80) cc_final: 0.7996 (t80) REVERT: C 1003 TYR cc_start: 0.6120 (m-80) cc_final: 0.4815 (m-10) REVERT: C 1032 TYR cc_start: 0.8303 (t80) cc_final: 0.7875 (t80) REVERT: D 405 TYR cc_start: 0.8231 (m-80) cc_final: 0.7897 (m-80) REVERT: D 407 MET cc_start: 0.5200 (mtm) cc_final: 0.4605 (mmp) REVERT: D 408 MET cc_start: 0.5509 (mmm) cc_final: 0.5209 (mmt) REVERT: D 414 MET cc_start: 0.5944 (mpp) cc_final: 0.5563 (mpp) REVERT: D 428 LEU cc_start: 0.8471 (mt) cc_final: 0.8001 (mt) REVERT: D 458 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8551 (mmmt) REVERT: D 463 MET cc_start: 0.7953 (mtm) cc_final: 0.7663 (mmm) REVERT: D 490 ASP cc_start: 0.8246 (m-30) cc_final: 0.7927 (m-30) REVERT: D 496 MET cc_start: 0.5421 (pmm) cc_final: 0.5023 (pmm) REVERT: D 503 MET cc_start: 0.7834 (ppp) cc_final: 0.7375 (ppp) REVERT: D 527 MET cc_start: 0.6567 (ttm) cc_final: 0.6143 (ttm) REVERT: D 629 MET cc_start: 0.6957 (mmm) cc_final: 0.6536 (tpp) REVERT: D 649 THR cc_start: 0.4580 (p) cc_final: 0.4309 (p) REVERT: D 760 ASP cc_start: 0.7106 (m-30) cc_final: 0.6800 (t0) REVERT: D 815 CYS cc_start: 0.6364 (m) cc_final: 0.5987 (t) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2775 time to fit residues: 143.1559 Evaluate side-chains 275 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 193 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.8848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16168 Z= 0.168 Angle : 0.605 9.342 21816 Z= 0.308 Chirality : 0.041 0.181 2454 Planarity : 0.004 0.066 2684 Dihedral : 5.925 58.779 2208 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1992 helix: 1.69 (0.16), residues: 1092 sheet: -1.19 (0.35), residues: 186 loop : -1.35 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 767 HIS 0.004 0.001 HIS C 950 PHE 0.033 0.001 PHE B 531 TYR 0.026 0.001 TYR A 711 ARG 0.004 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.7391 (t80) cc_final: 0.7089 (t80) REVERT: A 510 SER cc_start: 0.5682 (m) cc_final: 0.5351 (t) REVERT: A 527 MET cc_start: 0.6553 (mmt) cc_final: 0.6043 (tpp) REVERT: A 585 MET cc_start: 0.8368 (tpp) cc_final: 0.7600 (tpp) REVERT: A 586 GLN cc_start: 0.8287 (tp-100) cc_final: 0.7849 (tp40) REVERT: A 619 ASN cc_start: 0.7884 (t0) cc_final: 0.6942 (t0) REVERT: A 627 GLU cc_start: 0.8458 (tt0) cc_final: 0.7840 (tp30) REVERT: A 704 LEU cc_start: 0.8064 (pt) cc_final: 0.7016 (pt) REVERT: A 707 THR cc_start: 0.8407 (m) cc_final: 0.8192 (p) REVERT: A 939 MET cc_start: 0.6153 (ttt) cc_final: 0.4964 (tmm) REVERT: A 988 MET cc_start: 0.3718 (tpt) cc_final: 0.3401 (tpt) REVERT: A 1023 MET cc_start: 0.3415 (ptm) cc_final: 0.3187 (ptm) REVERT: B 460 TRP cc_start: 0.6741 (m100) cc_final: 0.6132 (m-90) REVERT: B 533 TYR cc_start: 0.8430 (t80) cc_final: 0.8160 (t80) REVERT: B 584 PHE cc_start: 0.9242 (t80) cc_final: 0.9029 (t80) REVERT: B 587 GLN cc_start: 0.7131 (mm110) cc_final: 0.6551 (mm-40) REVERT: B 708 MET cc_start: 0.8029 (mtt) cc_final: 0.7424 (tpt) REVERT: C 424 TYR cc_start: 0.7955 (t80) cc_final: 0.7432 (t80) REVERT: C 496 MET cc_start: 0.6312 (tpt) cc_final: 0.5947 (tpt) REVERT: C 606 TRP cc_start: 0.8627 (m-10) cc_final: 0.8398 (m-10) REVERT: C 607 PHE cc_start: 0.8827 (t80) cc_final: 0.8598 (t80) REVERT: C 637 GLU cc_start: 0.8494 (mp0) cc_final: 0.7899 (mp0) REVERT: C 668 ASP cc_start: 0.8752 (m-30) cc_final: 0.8475 (m-30) REVERT: C 670 MET cc_start: 0.8609 (mmm) cc_final: 0.8348 (mmm) REVERT: C 713 GLU cc_start: 0.8941 (pt0) cc_final: 0.8693 (pt0) REVERT: C 811 LEU cc_start: 0.9638 (tp) cc_final: 0.9331 (mt) REVERT: C 817 LYS cc_start: 0.8383 (tppp) cc_final: 0.7729 (ptmt) REVERT: C 840 LEU cc_start: 0.8824 (mt) cc_final: 0.8585 (mt) REVERT: C 861 TRP cc_start: 0.8026 (m100) cc_final: 0.7658 (m100) REVERT: C 882 LEU cc_start: 0.7381 (pp) cc_final: 0.6844 (pp) REVERT: C 939 MET cc_start: 0.8457 (ptp) cc_final: 0.8179 (tmm) REVERT: C 999 PHE cc_start: 0.8266 (t80) cc_final: 0.7933 (t80) REVERT: C 1032 TYR cc_start: 0.8284 (t80) cc_final: 0.7816 (t80) REVERT: D 414 MET cc_start: 0.6117 (mpp) cc_final: 0.5720 (mpp) REVERT: D 458 LYS cc_start: 0.8980 (mmtp) cc_final: 0.8508 (mmmt) REVERT: D 460 TRP cc_start: 0.4743 (m100) cc_final: 0.4094 (m100) REVERT: D 463 MET cc_start: 0.7718 (mtm) cc_final: 0.7458 (mtp) REVERT: D 490 ASP cc_start: 0.8083 (m-30) cc_final: 0.7792 (m-30) REVERT: D 527 MET cc_start: 0.6638 (ttm) cc_final: 0.6110 (ttm) REVERT: D 584 PHE cc_start: 0.8075 (t80) cc_final: 0.7372 (t80) REVERT: D 585 MET cc_start: 0.7059 (mmm) cc_final: 0.6802 (mmt) REVERT: D 647 TYR cc_start: 0.6909 (m-80) cc_final: 0.6708 (m-80) REVERT: D 670 MET cc_start: 0.8292 (tmm) cc_final: 0.7621 (tmm) REVERT: D 760 ASP cc_start: 0.7387 (m-30) cc_final: 0.6943 (t0) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2824 time to fit residues: 159.9450 Evaluate side-chains 300 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 117 optimal weight: 0.0870 chunk 88 optimal weight: 0.0980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 985 ASN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.9499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16168 Z= 0.146 Angle : 0.588 8.065 21816 Z= 0.300 Chirality : 0.040 0.153 2454 Planarity : 0.004 0.065 2684 Dihedral : 5.759 56.301 2208 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1992 helix: 1.76 (0.16), residues: 1090 sheet: -1.07 (0.34), residues: 194 loop : -1.38 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 767 HIS 0.003 0.001 HIS C 950 PHE 0.043 0.001 PHE C 531 TYR 0.014 0.001 TYR C 647 ARG 0.008 0.000 ARG A 991 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.7695 (t80) cc_final: 0.7103 (t80) REVERT: A 510 SER cc_start: 0.5764 (m) cc_final: 0.5468 (t) REVERT: A 585 MET cc_start: 0.8260 (tpp) cc_final: 0.7932 (mmt) REVERT: A 611 ILE cc_start: 0.8886 (mm) cc_final: 0.8661 (mm) REVERT: A 619 ASN cc_start: 0.8037 (t0) cc_final: 0.7116 (t0) REVERT: A 627 GLU cc_start: 0.8441 (tt0) cc_final: 0.7815 (tp30) REVERT: A 707 THR cc_start: 0.8537 (m) cc_final: 0.8248 (p) REVERT: A 921 VAL cc_start: 0.9277 (t) cc_final: 0.8927 (t) REVERT: A 939 MET cc_start: 0.6282 (ttt) cc_final: 0.5297 (tmm) REVERT: A 988 MET cc_start: 0.3860 (tpt) cc_final: 0.3642 (tpt) REVERT: B 460 TRP cc_start: 0.6722 (m100) cc_final: 0.6135 (m-90) REVERT: B 533 TYR cc_start: 0.8477 (t80) cc_final: 0.8137 (t80) REVERT: B 578 TRP cc_start: 0.8096 (t-100) cc_final: 0.7795 (t-100) REVERT: B 627 GLU cc_start: 0.8152 (pp20) cc_final: 0.7616 (tp30) REVERT: B 708 MET cc_start: 0.7829 (mtt) cc_final: 0.7095 (tpt) REVERT: B 795 VAL cc_start: 0.9079 (t) cc_final: 0.8859 (p) REVERT: C 424 TYR cc_start: 0.7955 (t80) cc_final: 0.7446 (t80) REVERT: C 431 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8701 (tp30) REVERT: C 496 MET cc_start: 0.6115 (tpt) cc_final: 0.5813 (tpt) REVERT: C 524 GLU cc_start: 0.9131 (mp0) cc_final: 0.8912 (mp0) REVERT: C 606 TRP cc_start: 0.8782 (m-10) cc_final: 0.8463 (m-10) REVERT: C 607 PHE cc_start: 0.8879 (t80) cc_final: 0.8651 (t80) REVERT: C 637 GLU cc_start: 0.8408 (mp0) cc_final: 0.8159 (mp0) REVERT: C 668 ASP cc_start: 0.8765 (m-30) cc_final: 0.8522 (m-30) REVERT: C 713 GLU cc_start: 0.8971 (pt0) cc_final: 0.8716 (pt0) REVERT: C 762 LEU cc_start: 0.9496 (mp) cc_final: 0.8881 (mp) REVERT: C 789 LEU cc_start: 0.9402 (tt) cc_final: 0.9201 (pp) REVERT: C 811 LEU cc_start: 0.9632 (tp) cc_final: 0.9350 (mt) REVERT: C 817 LYS cc_start: 0.8328 (tppp) cc_final: 0.7739 (ptmt) REVERT: C 840 LEU cc_start: 0.8758 (mt) cc_final: 0.8553 (mt) REVERT: C 879 LYS cc_start: 0.8027 (tptt) cc_final: 0.7507 (mttt) REVERT: C 1032 TYR cc_start: 0.8254 (t80) cc_final: 0.7807 (t80) REVERT: D 407 MET cc_start: 0.5812 (mtm) cc_final: 0.5288 (mmm) REVERT: D 408 MET cc_start: 0.5120 (mmm) cc_final: 0.4748 (mmm) REVERT: D 414 MET cc_start: 0.6199 (mpp) cc_final: 0.5848 (mpp) REVERT: D 428 LEU cc_start: 0.8365 (mm) cc_final: 0.8108 (mm) REVERT: D 458 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8613 (mmmt) REVERT: D 463 MET cc_start: 0.7844 (mtm) cc_final: 0.7513 (mmm) REVERT: D 490 ASP cc_start: 0.8186 (m-30) cc_final: 0.7933 (m-30) REVERT: D 493 LYS cc_start: 0.7626 (mptt) cc_final: 0.7325 (mppt) REVERT: D 527 MET cc_start: 0.6799 (ttm) cc_final: 0.6237 (ttm) REVERT: D 584 PHE cc_start: 0.8255 (t80) cc_final: 0.7997 (t80) REVERT: D 585 MET cc_start: 0.7294 (mmm) cc_final: 0.7062 (tpp) REVERT: D 647 TYR cc_start: 0.6957 (m-80) cc_final: 0.6677 (m-80) REVERT: D 670 MET cc_start: 0.8369 (tmm) cc_final: 0.7690 (tmm) REVERT: D 720 THR cc_start: 0.8331 (p) cc_final: 0.7732 (t) REVERT: D 760 ASP cc_start: 0.7131 (m-30) cc_final: 0.6803 (t0) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.2689 time to fit residues: 152.4212 Evaluate side-chains 292 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 0.0370 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 1.0269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16168 Z= 0.154 Angle : 0.597 8.634 21816 Z= 0.301 Chirality : 0.040 0.163 2454 Planarity : 0.004 0.068 2684 Dihedral : 5.699 56.333 2208 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1992 helix: 1.77 (0.16), residues: 1096 sheet: -0.98 (0.35), residues: 194 loop : -1.46 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 605 HIS 0.004 0.001 HIS C 883 PHE 0.036 0.002 PHE A 607 TYR 0.013 0.001 TYR B 711 ARG 0.006 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.7833 (t80) cc_final: 0.7200 (t80) REVERT: A 537 SER cc_start: 0.9073 (m) cc_final: 0.8771 (p) REVERT: A 579 PHE cc_start: 0.8630 (t80) cc_final: 0.8415 (t80) REVERT: A 587 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7623 (tp-100) REVERT: A 611 ILE cc_start: 0.9013 (mm) cc_final: 0.8806 (mm) REVERT: A 627 GLU cc_start: 0.8470 (tt0) cc_final: 0.7846 (tp30) REVERT: A 705 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8242 (mm-30) REVERT: A 707 THR cc_start: 0.8641 (m) cc_final: 0.8345 (p) REVERT: A 721 MET cc_start: 0.5436 (ppp) cc_final: 0.5034 (ppp) REVERT: A 939 MET cc_start: 0.6531 (ttt) cc_final: 0.5621 (tmm) REVERT: A 988 MET cc_start: 0.4108 (tpt) cc_final: 0.3868 (tpt) REVERT: B 406 VAL cc_start: 0.8282 (t) cc_final: 0.8064 (t) REVERT: B 460 TRP cc_start: 0.6711 (m100) cc_final: 0.6101 (m-90) REVERT: B 527 MET cc_start: 0.7135 (mmt) cc_final: 0.6524 (mmm) REVERT: B 578 TRP cc_start: 0.8418 (t-100) cc_final: 0.8085 (t-100) REVERT: B 587 GLN cc_start: 0.7597 (mm110) cc_final: 0.7309 (mm110) REVERT: B 620 LEU cc_start: 0.8916 (tt) cc_final: 0.8636 (tt) REVERT: B 627 GLU cc_start: 0.8189 (pp20) cc_final: 0.7847 (pp20) REVERT: B 708 MET cc_start: 0.7602 (mtt) cc_final: 0.6992 (tpp) REVERT: B 795 VAL cc_start: 0.9224 (t) cc_final: 0.8970 (p) REVERT: C 424 TYR cc_start: 0.7970 (t80) cc_final: 0.7515 (t80) REVERT: C 431 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8748 (tp30) REVERT: C 496 MET cc_start: 0.6204 (tpt) cc_final: 0.5965 (tpt) REVERT: C 594 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7477 (ptp-110) REVERT: C 606 TRP cc_start: 0.8905 (m-10) cc_final: 0.8430 (m-10) REVERT: C 607 PHE cc_start: 0.9095 (t80) cc_final: 0.8880 (t80) REVERT: C 637 GLU cc_start: 0.8355 (mp0) cc_final: 0.8007 (mp0) REVERT: C 657 GLU cc_start: 0.8171 (tt0) cc_final: 0.7076 (tm-30) REVERT: C 713 GLU cc_start: 0.8935 (pt0) cc_final: 0.8698 (pt0) REVERT: C 762 LEU cc_start: 0.9512 (mp) cc_final: 0.8977 (mp) REVERT: C 789 LEU cc_start: 0.9292 (tt) cc_final: 0.9043 (pt) REVERT: C 811 LEU cc_start: 0.9627 (tp) cc_final: 0.9347 (mt) REVERT: C 817 LYS cc_start: 0.8281 (tppp) cc_final: 0.7737 (pttt) REVERT: C 1032 TYR cc_start: 0.8258 (t80) cc_final: 0.7875 (t80) REVERT: D 414 MET cc_start: 0.6288 (mpp) cc_final: 0.6045 (mpp) REVERT: D 418 ASN cc_start: 0.4301 (t0) cc_final: 0.4052 (t0) REVERT: D 428 LEU cc_start: 0.8570 (mm) cc_final: 0.8360 (mm) REVERT: D 458 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8616 (mmmt) REVERT: D 463 MET cc_start: 0.7885 (mtm) cc_final: 0.7657 (mtp) REVERT: D 490 ASP cc_start: 0.8269 (m-30) cc_final: 0.8018 (m-30) REVERT: D 493 LYS cc_start: 0.7576 (mptt) cc_final: 0.7247 (mppt) REVERT: D 584 PHE cc_start: 0.8503 (t80) cc_final: 0.8185 (t80) REVERT: D 609 THR cc_start: 0.8378 (p) cc_final: 0.7760 (p) REVERT: D 612 ILE cc_start: 0.8859 (mm) cc_final: 0.8603 (mm) REVERT: D 629 MET cc_start: 0.6654 (mmm) cc_final: 0.5825 (tpp) REVERT: D 647 TYR cc_start: 0.7176 (m-80) cc_final: 0.6865 (m-80) REVERT: D 670 MET cc_start: 0.8469 (tmm) cc_final: 0.7815 (tmm) REVERT: D 720 THR cc_start: 0.8316 (p) cc_final: 0.7495 (t) REVERT: D 760 ASP cc_start: 0.7182 (m-30) cc_final: 0.6875 (t0) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.2630 time to fit residues: 147.9803 Evaluate side-chains 297 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 169 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN B 586 GLN B 756 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN D 508 GLN D 575 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 1.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 16168 Z= 0.464 Angle : 1.079 11.406 21816 Z= 0.567 Chirality : 0.056 0.257 2454 Planarity : 0.007 0.094 2684 Dihedral : 8.582 69.404 2208 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 32.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.38 % Favored : 93.52 % Rotamer: Outliers : 0.06 % Allowed : 1.41 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 5.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.18), residues: 1992 helix: -0.36 (0.15), residues: 1064 sheet: -1.92 (0.37), residues: 171 loop : -2.08 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.006 TRP D 767 HIS 0.010 0.003 HIS C 412 PHE 0.046 0.004 PHE B 607 TYR 0.042 0.004 TYR C 405 ARG 0.038 0.002 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.8077 (mm) cc_final: 0.7483 (mm) REVERT: A 424 TYR cc_start: 0.8984 (t80) cc_final: 0.8759 (t80) REVERT: A 487 GLU cc_start: 0.8939 (pm20) cc_final: 0.8586 (pm20) REVERT: A 540 LEU cc_start: 0.9500 (mm) cc_final: 0.9072 (tt) REVERT: A 586 GLN cc_start: 0.8212 (tp40) cc_final: 0.7756 (tp40) REVERT: A 629 MET cc_start: 0.9311 (mmt) cc_final: 0.8930 (mmt) REVERT: A 695 LYS cc_start: 0.9110 (tmmt) cc_final: 0.8616 (mtpt) REVERT: A 705 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8710 (mm-30) REVERT: A 796 PHE cc_start: 0.8861 (m-80) cc_final: 0.8437 (m-80) REVERT: A 849 LEU cc_start: 0.7654 (tp) cc_final: 0.7266 (tp) REVERT: A 939 MET cc_start: 0.8549 (ttt) cc_final: 0.8221 (tmm) REVERT: B 463 MET cc_start: 0.5988 (ptm) cc_final: 0.5289 (ppp) REVERT: B 527 MET cc_start: 0.8245 (mmt) cc_final: 0.7903 (mmm) REVERT: B 620 LEU cc_start: 0.9559 (tt) cc_final: 0.9319 (tt) REVERT: B 629 MET cc_start: 0.4558 (tpt) cc_final: 0.4249 (tpt) REVERT: B 708 MET cc_start: 0.8720 (mtt) cc_final: 0.8103 (tpt) REVERT: B 710 GLU cc_start: 0.8619 (mm-30) cc_final: 0.7800 (pp20) REVERT: B 721 MET cc_start: 0.8552 (tmm) cc_final: 0.7936 (tmm) REVERT: B 768 TYR cc_start: 0.6798 (m-80) cc_final: 0.6483 (m-80) REVERT: B 807 MET cc_start: 0.9230 (mtp) cc_final: 0.9001 (tmm) REVERT: B 811 LEU cc_start: 0.8756 (mm) cc_final: 0.8294 (mt) REVERT: C 408 MET cc_start: 0.8037 (tpt) cc_final: 0.7604 (tpt) REVERT: C 527 MET cc_start: 0.9092 (ptp) cc_final: 0.8671 (ptp) REVERT: C 531 PHE cc_start: 0.9529 (m-80) cc_final: 0.9272 (m-10) REVERT: C 575 ASN cc_start: 0.9328 (m110) cc_final: 0.9073 (m110) REVERT: C 581 LEU cc_start: 0.9422 (mt) cc_final: 0.9168 (mt) REVERT: C 587 GLN cc_start: 0.7135 (pp30) cc_final: 0.6927 (pp30) REVERT: C 612 ILE cc_start: 0.9679 (mm) cc_final: 0.9264 (pt) REVERT: C 616 TYR cc_start: 0.9384 (t80) cc_final: 0.8991 (t80) REVERT: C 620 LEU cc_start: 0.9181 (mt) cc_final: 0.8738 (mt) REVERT: C 657 GLU cc_start: 0.8416 (tt0) cc_final: 0.8125 (tm-30) REVERT: C 762 LEU cc_start: 0.9503 (mp) cc_final: 0.9233 (mp) REVERT: C 763 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7126 (mmtt) REVERT: C 807 MET cc_start: 0.8910 (tmm) cc_final: 0.8675 (tmm) REVERT: C 861 TRP cc_start: 0.8141 (m100) cc_final: 0.7383 (m100) REVERT: C 880 MET cc_start: 0.5979 (tmm) cc_final: 0.5761 (tmm) REVERT: C 939 MET cc_start: 0.8782 (ptp) cc_final: 0.8450 (ptt) REVERT: C 987 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8188 (tm-30) REVERT: C 1005 TRP cc_start: 0.7599 (p90) cc_final: 0.7050 (m-10) REVERT: C 1032 TYR cc_start: 0.8139 (t80) cc_final: 0.7775 (t80) REVERT: D 407 MET cc_start: 0.7371 (mpp) cc_final: 0.6797 (mpp) REVERT: D 428 LEU cc_start: 0.8462 (mm) cc_final: 0.8209 (mm) REVERT: D 463 MET cc_start: 0.8521 (mtm) cc_final: 0.8138 (mmm) REVERT: D 527 MET cc_start: 0.7954 (mtm) cc_final: 0.7584 (mmt) REVERT: D 540 LEU cc_start: 0.9375 (tp) cc_final: 0.9157 (tp) REVERT: D 585 MET cc_start: 0.8832 (tpp) cc_final: 0.8219 (mmt) REVERT: D 629 MET cc_start: 0.5872 (mmm) cc_final: 0.5017 (mmm) REVERT: D 667 PHE cc_start: 0.8177 (m-80) cc_final: 0.7922 (m-80) REVERT: D 670 MET cc_start: 0.8577 (tmm) cc_final: 0.8358 (tmm) REVERT: D 760 ASP cc_start: 0.7781 (m-30) cc_final: 0.7302 (t0) REVERT: D 784 THR cc_start: 0.8116 (t) cc_final: 0.7792 (m) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.2468 time to fit residues: 169.7087 Evaluate side-chains 321 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN B 586 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN C 985 ASN D 461 ASN D 575 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 1.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 16168 Z= 0.241 Angle : 0.738 14.142 21816 Z= 0.380 Chirality : 0.044 0.274 2454 Planarity : 0.005 0.067 2684 Dihedral : 6.994 57.145 2208 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % 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: -0.87 (0.18), residues: 1992 helix: 0.51 (0.16), residues: 1089 sheet: -1.51 (0.40), residues: 159 loop : -1.98 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D 578 HIS 0.011 0.002 HIS D 435 PHE 0.036 0.002 PHE C 531 TYR 0.016 0.002 TYR D 700 ARG 0.008 0.001 ARG A 684 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 421 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8636 (t80) cc_final: 0.8392 (t80) REVERT: A 524 GLU cc_start: 0.9485 (pm20) cc_final: 0.9176 (mp0) REVERT: A 540 LEU cc_start: 0.9481 (mm) cc_final: 0.9248 (tp) REVERT: A 586 GLN cc_start: 0.7938 (tp40) cc_final: 0.7639 (tm-30) REVERT: A 627 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8745 (mt-10) REVERT: A 629 MET cc_start: 0.9189 (mmt) cc_final: 0.8849 (mmt) REVERT: A 670 MET cc_start: 0.8327 (mmp) cc_final: 0.8099 (mmm) REVERT: A 674 MET cc_start: 0.8174 (ttt) cc_final: 0.7684 (ttt) REVERT: A 705 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8867 (mm-30) REVERT: A 708 MET cc_start: 0.8655 (ptt) cc_final: 0.8203 (mmm) REVERT: A 721 MET cc_start: 0.7430 (ppp) cc_final: 0.7211 (ppp) REVERT: A 787 LEU cc_start: 0.9192 (mt) cc_final: 0.8884 (mp) REVERT: A 796 PHE cc_start: 0.8904 (m-80) cc_final: 0.8545 (m-80) REVERT: A 938 PHE cc_start: 0.9288 (m-80) cc_final: 0.8952 (m-80) REVERT: A 939 MET cc_start: 0.8771 (ttt) cc_final: 0.8406 (mmt) REVERT: A 943 PHE cc_start: 0.8948 (t80) cc_final: 0.8384 (t80) REVERT: A 980 TYR cc_start: 0.8477 (t80) cc_final: 0.8244 (t80) REVERT: A 1005 TRP cc_start: 0.5432 (m100) cc_final: 0.4302 (t60) REVERT: B 460 TRP cc_start: 0.7348 (m100) cc_final: 0.6696 (m-90) REVERT: B 526 TRP cc_start: 0.8700 (m100) cc_final: 0.8433 (m100) REVERT: B 527 MET cc_start: 0.8150 (mmt) cc_final: 0.7738 (mmm) REVERT: B 541 PHE cc_start: 0.9071 (t80) cc_final: 0.8827 (t80) REVERT: B 708 MET cc_start: 0.8365 (mtt) cc_final: 0.7955 (tpp) REVERT: B 710 GLU cc_start: 0.8731 (mm-30) cc_final: 0.7865 (pp20) REVERT: B 721 MET cc_start: 0.8519 (tmm) cc_final: 0.8221 (tmm) REVERT: B 734 ILE cc_start: 0.7960 (mm) cc_final: 0.7706 (tp) REVERT: B 808 LEU cc_start: 0.9208 (mm) cc_final: 0.8698 (mm) REVERT: B 814 PHE cc_start: 0.8334 (t80) cc_final: 0.7926 (t80) REVERT: C 405 TYR cc_start: 0.8711 (m-80) cc_final: 0.8460 (m-80) REVERT: C 424 TYR cc_start: 0.8523 (t80) cc_final: 0.7788 (t80) REVERT: C 431 GLU cc_start: 0.8839 (tp30) cc_final: 0.8628 (tp30) REVERT: C 527 MET cc_start: 0.9009 (ptp) cc_final: 0.8467 (ttt) REVERT: C 531 PHE cc_start: 0.9424 (m-80) cc_final: 0.8795 (m-80) REVERT: C 581 LEU cc_start: 0.9372 (mt) cc_final: 0.8979 (mt) REVERT: C 620 LEU cc_start: 0.9131 (mt) cc_final: 0.8639 (mt) REVERT: C 625 THR cc_start: 0.9545 (p) cc_final: 0.9321 (p) REVERT: C 629 MET cc_start: 0.9414 (mtt) cc_final: 0.9194 (mtt) REVERT: C 762 LEU cc_start: 0.9502 (mp) cc_final: 0.8903 (mp) REVERT: C 861 TRP cc_start: 0.7703 (m100) cc_final: 0.6900 (m100) REVERT: C 939 MET cc_start: 0.8837 (ptp) cc_final: 0.8591 (ptt) REVERT: C 987 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8140 (tm-30) REVERT: C 1005 TRP cc_start: 0.7640 (p90) cc_final: 0.7043 (m-10) REVERT: D 407 MET cc_start: 0.6954 (mpp) cc_final: 0.6539 (mpp) REVERT: D 463 MET cc_start: 0.8136 (mtm) cc_final: 0.7655 (ttm) REVERT: D 480 THR cc_start: 0.8755 (m) cc_final: 0.8553 (p) REVERT: D 523 TYR cc_start: 0.8275 (m-10) cc_final: 0.7184 (t80) REVERT: D 585 MET cc_start: 0.8551 (tpp) cc_final: 0.7773 (mmt) REVERT: D 629 MET cc_start: 0.6298 (mmm) cc_final: 0.5771 (mmm) REVERT: D 670 MET cc_start: 0.8805 (tmm) cc_final: 0.8212 (tmm) REVERT: D 714 GLN cc_start: 0.5480 (tt0) cc_final: 0.4827 (tt0) REVERT: D 760 ASP cc_start: 0.7687 (m-30) cc_final: 0.7164 (t0) REVERT: D 767 TRP cc_start: 0.7722 (m100) cc_final: 0.7114 (m100) REVERT: D 784 THR cc_start: 0.8514 (t) cc_final: 0.8248 (m) outliers start: 1 outliers final: 0 residues processed: 422 average time/residue: 0.2358 time to fit residues: 154.8216 Evaluate side-chains 315 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 44 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 163 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN A 985 ASN B 508 GLN B 586 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.083279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.064265 restraints weight = 69953.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.065797 restraints weight = 51558.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.066879 restraints weight = 40701.739| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 1.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16168 Z= 0.185 Angle : 0.697 9.231 21816 Z= 0.352 Chirality : 0.043 0.244 2454 Planarity : 0.004 0.060 2684 Dihedral : 6.449 55.700 2208 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 5.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 1992 helix: 0.95 (0.16), residues: 1071 sheet: -1.75 (0.36), residues: 186 loop : -1.85 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 578 HIS 0.002 0.001 HIS C 950 PHE 0.036 0.002 PHE C 938 TYR 0.024 0.001 TYR B 616 ARG 0.006 0.001 ARG C 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3644.08 seconds wall clock time: 67 minutes 1.10 seconds (4021.10 seconds total)