Starting phenix.real_space_refine on Fri Mar 22 11:12:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/03_2024/3jbx_6487.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/03_2024/3jbx_6487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/03_2024/3jbx_6487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/03_2024/3jbx_6487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/03_2024/3jbx_6487.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/03_2024/3jbx_6487.pdb" } resolution = 3.4 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16666 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 112 5.49 5 Mg 4 5.21 5 S 106 5.16 5 C 10124 2.51 5 N 2948 2.21 5 O 3374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 992": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C TYR 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 848": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16670 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 524} Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 8, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 318} Chain: "C" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 524} Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "H" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "J" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "K" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "L" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2107 SG CYS A 749 93.964 80.081 63.615 1.00 33.47 S ATOM 2128 SG CYS A 752 96.115 82.432 64.621 1.00 57.22 S ATOM 9256 SG CYS C 749 55.638 25.828 62.765 1.00 53.94 S ATOM 9277 SG CYS C 752 53.932 23.158 64.357 1.00 64.33 S Time building chain proxies: 8.96, per 1000 atoms: 0.54 Number of scatterers: 16670 At special positions: 0 Unit cell: (151.29, 107.01, 111.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 112 15.00 Mg 4 11.99 O 3374 8.00 N 2948 7.00 C 10124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 752 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " Number of angles added : 4 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 34.9% alpha, 22.3% beta 35 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 5.85 Creating SS restraints... Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 518 through 526 removed outlier: 3.525A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 589 through 600 Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.552A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 814 through 835 removed outlier: 4.605A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 864 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 889 removed outlier: 3.578A pdb=" N VAL A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 917 removed outlier: 4.182A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 900 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 946 through 951 removed outlier: 3.618A pdb=" N TYR A 950 " --> pdb=" O PHE A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 962 Processing helix chain 'A' and resid 964 through 973 removed outlier: 3.520A pdb=" N GLU A 970 " --> pdb=" O PRO A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 985 through 998 removed outlier: 3.875A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 998 " --> pdb=" O ARG A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1018 removed outlier: 3.764A pdb=" N ASP A1008 " --> pdb=" O PHE A1004 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A1018 " --> pdb=" O TRP A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 526 removed outlier: 3.512A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 587 Processing helix chain 'C' and resid 589 through 600 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 686 through 705 Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.540A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 784 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 814 through 835 removed outlier: 4.076A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 removed outlier: 3.835A pdb=" N ALA C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 888 " --> pdb=" O ALA C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 912 removed outlier: 3.617A pdb=" N LEU C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 946 through 951 removed outlier: 3.514A pdb=" N TYR C 950 " --> pdb=" O PHE C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.779A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1018 removed outlier: 3.673A pdb=" N SER C1018 " --> pdb=" O TRP C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 3.872A pdb=" N PHE C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C1027 " --> pdb=" O LYS C1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 Processing sheet with id= A, first strand: chain 'A' and resid 537 through 539 removed outlier: 7.143A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE A 644 " --> pdb=" O PRO A 676 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 572 " --> pdb=" O PHE A 681 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 537 through 539 removed outlier: 7.143A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 620 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.040A pdb=" N PHE B 345 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 318 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.544A pdb=" N SER B 20 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 76 through 80 removed outlier: 6.687A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.530A pdb=" N GLU B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 141 through 147 Processing sheet with id= H, first strand: chain 'B' and resid 159 through 161 Processing sheet with id= I, first strand: chain 'B' and resid 209 through 212 removed outlier: 3.629A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 263 through 264 removed outlier: 3.976A pdb=" N CYS B 287 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 537 through 539 Processing sheet with id= L, first strand: chain 'C' and resid 554 through 555 removed outlier: 6.110A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 640 " --> pdb=" O MET C 680 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE C 651 " --> pdb=" O THR C 661 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR C 661 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 554 through 555 removed outlier: 6.110A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 640 " --> pdb=" O MET C 680 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.135A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 318 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.247A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 76 through 80 removed outlier: 5.597A pdb=" N GLY D 94 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER D 105 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG D 96 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER D 103 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 141 through 147 Processing sheet with id= R, first strand: chain 'D' and resid 159 through 161 Processing sheet with id= S, first strand: chain 'D' and resid 208 through 212 Processing sheet with id= T, first strand: chain 'D' and resid 263 through 265 removed outlier: 4.074A pdb=" N CYS D 287 " --> pdb=" O ARG D 302 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 6.85 Time building geometry restraints manager: 7.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2612 1.32 - 1.45: 5234 1.45 - 1.57: 9039 1.57 - 1.70: 225 1.70 - 1.83: 158 Bond restraints: 17268 Sorted by residual: bond pdb=" CA VAL D 9 " pdb=" CB VAL D 9 " ideal model delta sigma weight residual 1.540 1.595 -0.055 1.36e-02 5.41e+03 1.61e+01 bond pdb=" CA VAL B 9 " pdb=" CB VAL B 9 " ideal model delta sigma weight residual 1.540 1.594 -0.054 1.36e-02 5.41e+03 1.55e+01 bond pdb=" CA PRO B 339 " pdb=" C PRO B 339 " ideal model delta sigma weight residual 1.517 1.552 -0.035 9.30e-03 1.16e+04 1.42e+01 bond pdb=" C GLU C 731 " pdb=" O GLU C 731 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.22e-02 6.72e+03 1.15e+01 bond pdb=" CA VAL A 562 " pdb=" CB VAL A 562 " ideal model delta sigma weight residual 1.540 1.581 -0.041 1.36e-02 5.41e+03 9.16e+00 ... (remaining 17263 not shown) Histogram of bond angle deviations from ideal: 96.33 - 104.66: 709 104.66 - 112.99: 9293 112.99 - 121.33: 9230 121.33 - 129.66: 4428 129.66 - 137.99: 168 Bond angle restraints: 23828 Sorted by residual: angle pdb=" C ASN A 842 " pdb=" N PRO A 843 " pdb=" CA PRO A 843 " ideal model delta sigma weight residual 120.31 130.61 -10.30 9.80e-01 1.04e+00 1.11e+02 angle pdb=" O MET C 733 " pdb=" C MET C 733 " pdb=" N VAL C 734 " ideal model delta sigma weight residual 122.09 112.14 9.95 1.08e+00 8.57e-01 8.49e+01 angle pdb=" N PRO D 339 " pdb=" CA PRO D 339 " pdb=" C PRO D 339 " ideal model delta sigma weight residual 110.70 119.58 -8.88 1.22e+00 6.72e-01 5.30e+01 angle pdb=" C LEU B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.47 127.29 -7.82 1.16e+00 7.43e-01 4.54e+01 angle pdb=" N ARG A 999 " pdb=" CA ARG A 999 " pdb=" C ARG A 999 " ideal model delta sigma weight residual 111.24 119.81 -8.57 1.29e+00 6.01e-01 4.42e+01 ... (remaining 23823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.74: 8994 28.74 - 57.48: 998 57.48 - 86.22: 101 86.22 - 114.96: 5 114.96 - 143.70: 2 Dihedral angle restraints: 10100 sinusoidal: 4888 harmonic: 5212 Sorted by residual: dihedral pdb=" CD ARG A 992 " pdb=" NE ARG A 992 " pdb=" CZ ARG A 992 " pdb=" NH1 ARG A 992 " ideal model delta sinusoidal sigma weight residual 0.00 71.05 -71.05 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CA LYS B 86 " pdb=" C LYS B 86 " pdb=" N PRO B 87 " pdb=" CA PRO B 87 " ideal model delta harmonic sigma weight residual -180.00 -143.29 -36.71 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA ALA C1027 " pdb=" C ALA C1027 " pdb=" N HIS C1028 " pdb=" CA HIS C1028 " ideal model delta harmonic sigma weight residual -180.00 -146.82 -33.18 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 10097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2366 0.083 - 0.165: 216 0.165 - 0.248: 14 0.248 - 0.331: 2 0.331 - 0.414: 2 Chirality restraints: 2600 Sorted by residual: chirality pdb=" CA ASN C 997 " pdb=" N ASN C 997 " pdb=" C ASN C 997 " pdb=" CB ASN C 997 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA MET C 996 " pdb=" N MET C 996 " pdb=" C MET C 996 " pdb=" CB MET C 996 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA ASN A 997 " pdb=" N ASN A 997 " pdb=" C ASN A 997 " pdb=" CB ASN A 997 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2597 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 992 " 1.045 9.50e-02 1.11e+02 4.68e-01 1.32e+02 pdb=" NE ARG A 992 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 992 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 992 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 992 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 870 " 0.864 9.50e-02 1.11e+02 3.87e-01 9.10e+01 pdb=" NE ARG C 870 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG C 870 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 870 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 870 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 994 " -0.672 9.50e-02 1.11e+02 3.01e-01 5.53e+01 pdb=" NE ARG C 994 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG C 994 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 994 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 994 " -0.021 2.00e-02 2.50e+03 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 74 2.43 - 3.05: 10294 3.05 - 3.67: 26614 3.67 - 4.28: 40020 4.28 - 4.90: 63308 Nonbonded interactions: 140310 Sorted by model distance: nonbonded pdb=" OE2 GLU C 731 " pdb=" NZ LYS C 960 " model vdw 1.816 2.520 nonbonded pdb=" O LEU A 481 " pdb=" NE2 GLN A 517 " model vdw 2.168 2.520 nonbonded pdb=" O3' DG F 15 " pdb="MG MG C1102 " model vdw 2.170 2.170 nonbonded pdb=" NE2 GLN A 858 " pdb=" O ALA A 887 " model vdw 2.172 2.520 nonbonded pdb=" NZ LYS C1011 " pdb=" OP1 DC H 8 " model vdw 2.173 2.520 ... (remaining 140305 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' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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 individual isotropic 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 2.640 Check model and map are aligned: 0.260 Set scattering table: 0.190 Process input model: 53.450 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.120 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17268 Z= 0.355 Angle : 1.238 13.563 23828 Z= 0.828 Chirality : 0.049 0.414 2600 Planarity : 0.014 0.468 2682 Dihedral : 21.203 143.696 6748 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 11.74 % Allowed : 11.81 % Favored : 76.45 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.15), residues: 1794 helix: -2.86 (0.16), residues: 550 sheet: -0.37 (0.25), residues: 296 loop : -2.12 (0.15), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 978 HIS 0.006 0.001 HIS B 269 PHE 0.032 0.002 PHE C1004 TYR 0.029 0.002 TYR C 729 ARG 0.004 0.001 ARG C 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 460 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.8975 (t) cc_final: 0.8705 (m) REVERT: A 690 LEU cc_start: 0.8448 (tp) cc_final: 0.7967 (tp) REVERT: A 730 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7309 (p0) REVERT: A 732 LYS cc_start: 0.8896 (tttt) cc_final: 0.8565 (ttmt) REVERT: A 749 CYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7663 (m) REVERT: A 792 ASP cc_start: 0.8242 (t0) cc_final: 0.8002 (t0) REVERT: A 814 ASP cc_start: 0.8250 (t0) cc_final: 0.7875 (t0) REVERT: A 833 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: A 863 MET cc_start: 0.8187 (mmp) cc_final: 0.7255 (tpp) REVERT: A 902 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8162 (mt) REVERT: A 981 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 11 CYS cc_start: 0.8000 (m) cc_final: 0.6777 (m) REVERT: B 33 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: B 80 PHE cc_start: 0.8531 (t80) cc_final: 0.8185 (t80) REVERT: B 192 CYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7689 (p) REVERT: B 200 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8041 (mp) REVERT: B 212 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6598 (ttp-170) REVERT: B 281 THR cc_start: 0.8405 (m) cc_final: 0.8169 (p) REVERT: B 285 MET cc_start: 0.8577 (mmm) cc_final: 0.8254 (mmm) REVERT: B 338 THR cc_start: 0.8425 (m) cc_final: 0.8150 (p) REVERT: C 487 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8196 (tp) REVERT: C 548 SER cc_start: 0.9121 (t) cc_final: 0.8739 (m) REVERT: C 571 THR cc_start: 0.7806 (m) cc_final: 0.7604 (t) REVERT: C 578 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.6811 (t80) REVERT: C 622 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7419 (ptp) REVERT: C 677 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8577 (tp) REVERT: C 680 MET cc_start: 0.8082 (mtm) cc_final: 0.7734 (mtp) REVERT: C 860 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8355 (ttm-80) REVERT: C 902 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8286 (mt) REVERT: C 1007 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: D 65 ASN cc_start: 0.8286 (p0) cc_final: 0.8005 (p0) REVERT: D 89 CYS cc_start: 0.8704 (t) cc_final: 0.8499 (t) REVERT: D 171 ASN cc_start: 0.8091 (m-40) cc_final: 0.7699 (p0) REVERT: D 186 ASP cc_start: 0.7895 (t0) cc_final: 0.7665 (t0) REVERT: D 224 LEU cc_start: 0.7953 (tp) cc_final: 0.7711 (tp) REVERT: D 250 THR cc_start: 0.8979 (t) cc_final: 0.8757 (p) REVERT: D 272 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7696 (tt) outliers start: 186 outliers final: 41 residues processed: 593 average time/residue: 0.3098 time to fit residues: 266.3329 Evaluate side-chains 322 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 266 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.0470 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 0.0980 chunk 170 optimal weight: 6.9990 overall best weight: 0.4880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN A1000 GLN B 4 GLN B 33 GLN B 64 ASN B 170 GLN C 492 ASN C 517 GLN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 997 ASN C1000 GLN D 100 ASN D 173 ASN D 222 HIS D 269 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17268 Z= 0.222 Angle : 0.767 12.356 23828 Z= 0.416 Chirality : 0.044 0.224 2600 Planarity : 0.006 0.064 2682 Dihedral : 22.511 153.788 3332 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.56 % Favored : 97.32 % Rotamer: Outliers : 6.12 % Allowed : 17.74 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -1.65 (0.17), residues: 1794 helix: -0.68 (0.21), residues: 528 sheet: -0.19 (0.26), residues: 314 loop : -1.67 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 851 HIS 0.008 0.001 HIS B 269 PHE 0.017 0.002 PHE D 350 TYR 0.020 0.002 TYR B 271 ARG 0.010 0.001 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 336 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 GLU cc_start: 0.7389 (pt0) cc_final: 0.7041 (pt0) REVERT: A 548 SER cc_start: 0.9119 (t) cc_final: 0.8867 (m) REVERT: A 578 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7321 (t80) REVERT: A 680 MET cc_start: 0.8183 (mtp) cc_final: 0.7825 (mtm) REVERT: A 730 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7082 (p0) REVERT: A 795 ARG cc_start: 0.8594 (ttp80) cc_final: 0.7643 (ttp80) REVERT: A 833 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: A 940 ASP cc_start: 0.8573 (p0) cc_final: 0.7715 (m-30) REVERT: A 968 ILE cc_start: 0.8517 (mt) cc_final: 0.8255 (mt) REVERT: B 11 CYS cc_start: 0.6997 (m) cc_final: 0.6751 (m) REVERT: B 80 PHE cc_start: 0.8484 (t80) cc_final: 0.8071 (t80) REVERT: B 177 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7694 (m-30) REVERT: B 186 ASP cc_start: 0.7846 (t0) cc_final: 0.7537 (t0) REVERT: B 192 CYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7737 (p) REVERT: B 232 ARG cc_start: 0.8858 (tmm-80) cc_final: 0.8514 (ttp80) REVERT: B 252 LEU cc_start: 0.8303 (mm) cc_final: 0.7857 (mt) REVERT: B 285 MET cc_start: 0.8494 (mmm) cc_final: 0.8064 (mmm) REVERT: C 548 SER cc_start: 0.9015 (t) cc_final: 0.8635 (m) REVERT: C 578 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7356 (t80) REVERT: C 680 MET cc_start: 0.7802 (mtm) cc_final: 0.7483 (mtp) REVERT: C 782 TRP cc_start: 0.8675 (OUTLIER) cc_final: 0.8311 (t-100) REVERT: C 1007 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: D 65 ASN cc_start: 0.8356 (p0) cc_final: 0.8060 (p0) REVERT: D 217 TYR cc_start: 0.7313 (m-80) cc_final: 0.6806 (m-10) outliers start: 97 outliers final: 45 residues processed: 404 average time/residue: 0.3014 time to fit residues: 178.4148 Evaluate side-chains 314 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 261 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 806 PHE Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 0.0270 chunk 47 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 169 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 137 optimal weight: 0.0370 overall best weight: 1.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS C 492 ASN C 858 GLN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17268 Z= 0.241 Angle : 0.692 11.761 23828 Z= 0.377 Chirality : 0.043 0.248 2600 Planarity : 0.005 0.068 2682 Dihedral : 22.334 151.949 3279 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.57 % Favored : 96.32 % Rotamer: Outliers : 5.24 % Allowed : 20.33 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -1.12 (0.18), residues: 1794 helix: -0.02 (0.22), residues: 534 sheet: -0.11 (0.26), residues: 342 loop : -1.42 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 317 HIS 0.008 0.001 HIS D 140 PHE 0.016 0.001 PHE B 350 TYR 0.022 0.002 TYR A 931 ARG 0.010 0.001 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 295 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9225 (t) cc_final: 0.8938 (m) REVERT: A 578 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7394 (t80) REVERT: A 675 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7479 (mtp85) REVERT: A 680 MET cc_start: 0.8249 (mtp) cc_final: 0.7868 (mtm) REVERT: A 690 LEU cc_start: 0.8708 (tp) cc_final: 0.8416 (tp) REVERT: A 730 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.6905 (p0) REVERT: A 749 CYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7492 (m) REVERT: A 795 ARG cc_start: 0.8494 (ttp80) cc_final: 0.7788 (ttp80) REVERT: A 833 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 902 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8291 (mt) REVERT: A 981 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7478 (mm-30) REVERT: B 80 PHE cc_start: 0.8462 (t80) cc_final: 0.8059 (t80) REVERT: B 113 SER cc_start: 0.8529 (m) cc_final: 0.8228 (p) REVERT: B 177 ASP cc_start: 0.7934 (m-30) cc_final: 0.7690 (m-30) REVERT: B 186 ASP cc_start: 0.7850 (t0) cc_final: 0.7541 (t0) REVERT: B 252 LEU cc_start: 0.8316 (mm) cc_final: 0.7821 (mt) REVERT: C 548 SER cc_start: 0.9170 (t) cc_final: 0.8809 (m) REVERT: C 578 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7677 (t80) REVERT: C 677 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8545 (tp) REVERT: C 680 MET cc_start: 0.8062 (mtm) cc_final: 0.7690 (mtp) REVERT: C 782 TRP cc_start: 0.8657 (OUTLIER) cc_final: 0.8321 (t-100) REVERT: C 882 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7522 (ttt-90) REVERT: C 905 MET cc_start: 0.8028 (tpp) cc_final: 0.7234 (tpp) REVERT: C 981 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7635 (mm-30) REVERT: C 1007 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: D 65 ASN cc_start: 0.8396 (p0) cc_final: 0.8061 (p0) REVERT: D 132 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.5849 (m-30) REVERT: D 162 MET cc_start: 0.8449 (mtt) cc_final: 0.8197 (mtt) REVERT: D 232 ARG cc_start: 0.8458 (tmm-80) cc_final: 0.8240 (ttp80) outliers start: 83 outliers final: 50 residues processed: 346 average time/residue: 0.2990 time to fit residues: 153.8191 Evaluate side-chains 314 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 254 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 81 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 171 optimal weight: 0.5980 chunk 181 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1028 HIS D 99 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17268 Z= 0.243 Angle : 0.671 12.077 23828 Z= 0.363 Chirality : 0.043 0.200 2600 Planarity : 0.005 0.069 2682 Dihedral : 22.266 156.106 3271 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 6.38 % Allowed : 19.82 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.87 (0.19), residues: 1794 helix: 0.24 (0.22), residues: 538 sheet: -0.04 (0.26), residues: 352 loop : -1.29 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 317 HIS 0.008 0.001 HIS A 964 PHE 0.014 0.002 PHE D 189 TYR 0.016 0.002 TYR A 931 ARG 0.011 0.001 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 280 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9309 (t) cc_final: 0.9039 (m) REVERT: A 578 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7257 (t80) REVERT: A 664 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: A 680 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7978 (mtp) REVERT: A 690 LEU cc_start: 0.8685 (tp) cc_final: 0.8396 (tp) REVERT: A 730 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.6990 (p0) REVERT: A 795 ARG cc_start: 0.8457 (ttp80) cc_final: 0.7721 (ttp80) REVERT: A 833 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: A 863 MET cc_start: 0.8449 (mmm) cc_final: 0.8169 (tpp) REVERT: A 905 MET cc_start: 0.8223 (tpp) cc_final: 0.7587 (tpp) REVERT: B 54 GLU cc_start: 0.8079 (tp30) cc_final: 0.7866 (tp30) REVERT: B 80 PHE cc_start: 0.8423 (t80) cc_final: 0.8034 (t80) REVERT: B 113 SER cc_start: 0.8400 (m) cc_final: 0.8169 (p) REVERT: B 177 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: B 232 ARG cc_start: 0.8964 (tmm-80) cc_final: 0.8676 (tmm-80) REVERT: B 285 MET cc_start: 0.8580 (mmt) cc_final: 0.8133 (mmm) REVERT: B 324 LYS cc_start: 0.7619 (mtpt) cc_final: 0.7394 (tttt) REVERT: C 548 SER cc_start: 0.9163 (t) cc_final: 0.8828 (m) REVERT: C 677 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8564 (tp) REVERT: C 680 MET cc_start: 0.8143 (mtm) cc_final: 0.7773 (mtp) REVERT: C 782 TRP cc_start: 0.8694 (OUTLIER) cc_final: 0.8406 (t-100) REVERT: C 905 MET cc_start: 0.8077 (tpp) cc_final: 0.7120 (tpp) REVERT: C 1007 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: D 65 ASN cc_start: 0.8395 (p0) cc_final: 0.8057 (p0) REVERT: D 132 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6084 (m-30) REVERT: D 162 MET cc_start: 0.8360 (mtt) cc_final: 0.8158 (mtt) REVERT: D 233 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8119 (mp) outliers start: 101 outliers final: 60 residues processed: 349 average time/residue: 0.2919 time to fit residues: 151.6521 Evaluate side-chains 311 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 240 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 155 optimal weight: 0.3980 chunk 125 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS C 492 ASN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17268 Z= 0.184 Angle : 0.642 12.687 23828 Z= 0.345 Chirality : 0.041 0.209 2600 Planarity : 0.005 0.068 2682 Dihedral : 22.022 159.442 3263 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.01 % Favored : 95.88 % Rotamer: Outliers : 5.30 % Allowed : 21.34 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.69 (0.19), residues: 1794 helix: 0.45 (0.22), residues: 540 sheet: 0.07 (0.26), residues: 364 loop : -1.25 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 317 HIS 0.005 0.001 HIS D 140 PHE 0.013 0.001 PHE C 826 TYR 0.021 0.002 TYR C 504 ARG 0.006 0.000 ARG C 882 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 281 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9298 (t) cc_final: 0.9036 (m) REVERT: A 578 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7193 (t80) REVERT: A 680 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7842 (mtp) REVERT: A 730 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7344 (p0) REVERT: A 833 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: A 905 MET cc_start: 0.8262 (tpp) cc_final: 0.7496 (tpp) REVERT: B 34 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8038 (ttmt) REVERT: B 54 GLU cc_start: 0.7917 (tp30) cc_final: 0.7609 (tp30) REVERT: B 80 PHE cc_start: 0.8392 (t80) cc_final: 0.8026 (t80) REVERT: B 177 ASP cc_start: 0.7967 (m-30) cc_final: 0.7754 (m-30) REVERT: B 186 ASP cc_start: 0.7798 (t0) cc_final: 0.7492 (t0) REVERT: B 252 LEU cc_start: 0.8234 (mm) cc_final: 0.7870 (mt) REVERT: B 285 MET cc_start: 0.8565 (mmt) cc_final: 0.8179 (mmm) REVERT: C 548 SER cc_start: 0.9120 (t) cc_final: 0.8802 (m) REVERT: C 578 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7828 (t80) REVERT: C 622 MET cc_start: 0.7891 (ptp) cc_final: 0.7677 (ptm) REVERT: C 677 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8460 (tp) REVERT: C 680 MET cc_start: 0.8033 (mtm) cc_final: 0.7624 (mtp) REVERT: C 731 GLU cc_start: 0.7673 (tt0) cc_final: 0.7468 (tt0) REVERT: C 782 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.8417 (t-100) REVERT: C 880 MET cc_start: 0.8024 (mmm) cc_final: 0.7670 (mmm) REVERT: D 132 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6016 (m-30) REVERT: D 162 MET cc_start: 0.8290 (mtt) cc_final: 0.8025 (mtt) REVERT: D 186 ASP cc_start: 0.7195 (t0) cc_final: 0.6932 (t0) REVERT: D 189 PHE cc_start: 0.6306 (m-10) cc_final: 0.5970 (m-10) REVERT: D 285 MET cc_start: 0.8257 (mmt) cc_final: 0.7765 (mmm) outliers start: 84 outliers final: 51 residues processed: 337 average time/residue: 0.2724 time to fit residues: 139.1192 Evaluate side-chains 320 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 260 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 HIS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS C 492 ASN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17268 Z= 0.337 Angle : 0.698 12.169 23828 Z= 0.376 Chirality : 0.044 0.202 2600 Planarity : 0.005 0.069 2682 Dihedral : 22.154 157.631 3260 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 5.49 % Allowed : 21.91 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.70 (0.19), residues: 1794 helix: 0.42 (0.22), residues: 548 sheet: 0.04 (0.27), residues: 350 loop : -1.23 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 317 HIS 0.037 0.002 HIS B 298 PHE 0.017 0.002 PHE D 62 TYR 0.032 0.002 TYR A 578 ARG 0.007 0.001 ARG C 882 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 261 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9353 (t) cc_final: 0.9083 (m) REVERT: A 680 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8093 (mtp) REVERT: A 730 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7517 (p0) REVERT: A 833 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: A 902 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8236 (mt) REVERT: B 80 PHE cc_start: 0.8423 (t80) cc_final: 0.8060 (t80) REVERT: B 186 ASP cc_start: 0.7705 (t0) cc_final: 0.7470 (t0) REVERT: C 578 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7946 (t80) REVERT: C 677 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8448 (tp) REVERT: C 680 MET cc_start: 0.8161 (mtm) cc_final: 0.7636 (mtp) REVERT: C 748 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7910 (pt) REVERT: C 782 TRP cc_start: 0.8675 (OUTLIER) cc_final: 0.8444 (t-100) REVERT: C 905 MET cc_start: 0.8113 (tpp) cc_final: 0.7251 (tpp) REVERT: D 132 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6033 (m-30) REVERT: D 162 MET cc_start: 0.8378 (mtt) cc_final: 0.7605 (mtm) REVERT: D 171 ASN cc_start: 0.8351 (p0) cc_final: 0.8118 (p0) REVERT: D 274 PHE cc_start: 0.7651 (t80) cc_final: 0.7400 (t80) outliers start: 87 outliers final: 59 residues processed: 318 average time/residue: 0.2713 time to fit residues: 132.0278 Evaluate side-chains 311 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 243 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 204 GLN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17268 Z= 0.204 Angle : 0.644 13.027 23828 Z= 0.346 Chirality : 0.041 0.201 2600 Planarity : 0.005 0.068 2682 Dihedral : 21.993 155.543 3254 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.93 % Rotamer: Outliers : 4.80 % Allowed : 23.61 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.58 (0.19), residues: 1794 helix: 0.49 (0.23), residues: 538 sheet: 0.11 (0.27), residues: 364 loop : -1.13 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 317 HIS 0.005 0.001 HIS D 140 PHE 0.020 0.001 PHE D 350 TYR 0.024 0.002 TYR C 931 ARG 0.007 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 269 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9317 (t) cc_final: 0.9038 (m) REVERT: A 680 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: A 730 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7342 (p0) REVERT: A 833 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: B 34 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7894 (ttmt) REVERT: B 80 PHE cc_start: 0.8390 (t80) cc_final: 0.8050 (t80) REVERT: B 186 ASP cc_start: 0.7755 (t0) cc_final: 0.7451 (t0) REVERT: B 285 MET cc_start: 0.8632 (mmt) cc_final: 0.8166 (mmm) REVERT: C 578 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7822 (t80) REVERT: C 677 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8371 (tp) REVERT: C 680 MET cc_start: 0.7996 (mtm) cc_final: 0.7588 (mtp) REVERT: C 731 GLU cc_start: 0.7798 (tt0) cc_final: 0.7581 (tt0) REVERT: C 981 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7752 (tp30) REVERT: D 132 ASP cc_start: 0.6815 (OUTLIER) cc_final: 0.5983 (m-30) REVERT: D 162 MET cc_start: 0.8322 (mtt) cc_final: 0.7561 (mtm) REVERT: D 171 ASN cc_start: 0.8458 (p0) cc_final: 0.8206 (p0) outliers start: 76 outliers final: 48 residues processed: 320 average time/residue: 0.2748 time to fit residues: 133.8372 Evaluate side-chains 310 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 255 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.0980 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 0.0870 chunk 35 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 123 optimal weight: 0.0270 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.0418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN C 492 ASN C 956 ASN D 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17268 Z= 0.199 Angle : 0.641 13.016 23828 Z= 0.344 Chirality : 0.041 0.199 2600 Planarity : 0.005 0.067 2682 Dihedral : 21.917 155.092 3252 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 4.36 % Allowed : 24.12 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: 1794 helix: 0.57 (0.23), residues: 536 sheet: 0.18 (0.27), residues: 364 loop : -1.08 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 317 HIS 0.005 0.001 HIS D 140 PHE 0.017 0.001 PHE D 189 TYR 0.021 0.002 TYR C 931 ARG 0.011 0.001 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 265 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9332 (t) cc_final: 0.9041 (m) REVERT: A 647 MET cc_start: 0.7693 (mmt) cc_final: 0.7349 (mmm) REVERT: A 680 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7982 (mtp) REVERT: A 730 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7335 (p0) REVERT: A 813 LEU cc_start: 0.8137 (tt) cc_final: 0.7925 (tp) REVERT: A 833 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: A 902 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8273 (mt) REVERT: A 905 MET cc_start: 0.7825 (tpp) cc_final: 0.7610 (ttp) REVERT: B 34 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7880 (ttmt) REVERT: B 54 GLU cc_start: 0.7941 (tp30) cc_final: 0.7730 (tp30) REVERT: B 80 PHE cc_start: 0.8348 (t80) cc_final: 0.8025 (t80) REVERT: B 171 ASN cc_start: 0.7512 (p0) cc_final: 0.7194 (p0) REVERT: B 186 ASP cc_start: 0.7824 (t0) cc_final: 0.7506 (t0) REVERT: B 285 MET cc_start: 0.8670 (mmt) cc_final: 0.8168 (mmm) REVERT: C 578 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7800 (t80) REVERT: C 677 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8307 (tp) REVERT: C 680 MET cc_start: 0.8031 (mtm) cc_final: 0.7638 (mtp) REVERT: C 690 LEU cc_start: 0.8325 (tp) cc_final: 0.7978 (tt) REVERT: C 701 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8416 (ttp80) REVERT: C 880 MET cc_start: 0.8422 (tpp) cc_final: 0.7587 (mmm) REVERT: D 132 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.5830 (m-30) REVERT: D 162 MET cc_start: 0.8307 (mtt) cc_final: 0.7558 (mtm) REVERT: D 171 ASN cc_start: 0.8480 (p0) cc_final: 0.8232 (p0) REVERT: D 285 MET cc_start: 0.8317 (mmt) cc_final: 0.7623 (mmm) outliers start: 69 outliers final: 48 residues processed: 315 average time/residue: 0.2634 time to fit residues: 128.3198 Evaluate side-chains 306 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 249 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17268 Z= 0.333 Angle : 0.697 12.635 23828 Z= 0.373 Chirality : 0.043 0.205 2600 Planarity : 0.005 0.068 2682 Dihedral : 22.051 154.945 3250 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.85 % Favored : 95.04 % Rotamer: Outliers : 4.48 % Allowed : 24.75 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.61 (0.19), residues: 1794 helix: 0.41 (0.22), residues: 552 sheet: 0.18 (0.27), residues: 348 loop : -1.15 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 317 HIS 0.007 0.001 HIS D 140 PHE 0.030 0.002 PHE B 62 TYR 0.024 0.002 TYR A 578 ARG 0.014 0.001 ARG C 598 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 250 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9353 (t) cc_final: 0.9055 (m) REVERT: A 647 MET cc_start: 0.7817 (mmt) cc_final: 0.7443 (mmm) REVERT: A 680 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8069 (mtp) REVERT: A 730 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7556 (p0) REVERT: A 833 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: A 902 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8287 (mt) REVERT: B 34 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7999 (ttmt) REVERT: B 80 PHE cc_start: 0.8417 (t80) cc_final: 0.7866 (t80) REVERT: B 171 ASN cc_start: 0.7859 (p0) cc_final: 0.7401 (p0) REVERT: B 186 ASP cc_start: 0.7730 (t0) cc_final: 0.7513 (t0) REVERT: C 578 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7862 (t80) REVERT: C 677 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8389 (tp) REVERT: C 680 MET cc_start: 0.8085 (mtm) cc_final: 0.7280 (mtm) REVERT: C 701 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8416 (ttp80) REVERT: D 80 PHE cc_start: 0.8121 (t80) cc_final: 0.7730 (t80) REVERT: D 132 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6332 (m-30) REVERT: D 162 MET cc_start: 0.8356 (mtt) cc_final: 0.7633 (mtm) REVERT: D 171 ASN cc_start: 0.8538 (p0) cc_final: 0.8244 (p0) REVERT: D 269 HIS cc_start: 0.6912 (t70) cc_final: 0.6672 (t-170) outliers start: 71 outliers final: 53 residues processed: 298 average time/residue: 0.2673 time to fit residues: 122.6426 Evaluate side-chains 310 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 248 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 951 ASP Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17268 Z= 0.192 Angle : 0.647 13.454 23828 Z= 0.347 Chirality : 0.041 0.202 2600 Planarity : 0.005 0.066 2682 Dihedral : 21.806 154.503 3250 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % Rotamer: Outliers : 3.66 % Allowed : 25.69 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.46 (0.19), residues: 1794 helix: 0.60 (0.22), residues: 548 sheet: 0.25 (0.27), residues: 362 loop : -1.11 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 317 HIS 0.005 0.001 HIS D 140 PHE 0.019 0.001 PHE D 189 TYR 0.022 0.002 TYR C 504 ARG 0.012 0.001 ARG B 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 272 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 SER cc_start: 0.9320 (t) cc_final: 0.9063 (m) REVERT: A 647 MET cc_start: 0.7797 (mmt) cc_final: 0.7534 (mmm) REVERT: A 680 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7957 (mtp) REVERT: A 730 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7311 (p0) REVERT: A 813 LEU cc_start: 0.8151 (tt) cc_final: 0.7912 (tp) REVERT: A 833 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: A 871 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8186 (tpp) REVERT: A 902 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8260 (mt) REVERT: B 34 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7906 (ttmt) REVERT: B 61 SER cc_start: 0.8498 (m) cc_final: 0.8273 (p) REVERT: B 80 PHE cc_start: 0.8355 (t80) cc_final: 0.8021 (t80) REVERT: B 171 ASN cc_start: 0.7768 (p0) cc_final: 0.7513 (p0) REVERT: B 186 ASP cc_start: 0.7752 (t0) cc_final: 0.7547 (t0) REVERT: B 285 MET cc_start: 0.8684 (mmt) cc_final: 0.8201 (mmm) REVERT: C 578 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7820 (t80) REVERT: C 675 ARG cc_start: 0.7279 (mmm160) cc_final: 0.6894 (mmt-90) REVERT: C 677 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8285 (tp) REVERT: C 680 MET cc_start: 0.8021 (mtm) cc_final: 0.7581 (mtp) REVERT: C 701 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8439 (ttp80) REVERT: C 905 MET cc_start: 0.8129 (tpp) cc_final: 0.7120 (tpp) REVERT: D 80 PHE cc_start: 0.8104 (t80) cc_final: 0.7780 (t80) REVERT: D 113 SER cc_start: 0.8275 (m) cc_final: 0.8069 (p) REVERT: D 132 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6267 (m-30) REVERT: D 162 MET cc_start: 0.8292 (mtt) cc_final: 0.7595 (mtm) REVERT: D 285 MET cc_start: 0.8430 (mmt) cc_final: 0.8022 (mmm) outliers start: 58 outliers final: 42 residues processed: 307 average time/residue: 0.2664 time to fit residues: 124.9355 Evaluate side-chains 306 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 254 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 560 TRP Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 955 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 985 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116501 restraints weight = 26361.000| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.37 r_work: 0.3380 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17268 Z= 0.191 Angle : 0.649 13.809 23828 Z= 0.348 Chirality : 0.041 0.205 2600 Planarity : 0.005 0.068 2682 Dihedral : 21.688 154.642 3250 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.46 % Favored : 95.43 % Rotamer: Outliers : 3.54 % Allowed : 26.39 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.46 % Twisted Proline : 1.11 % 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: -0.42 (0.19), residues: 1794 helix: 0.68 (0.22), residues: 548 sheet: 0.17 (0.27), residues: 372 loop : -1.08 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 317 HIS 0.010 0.001 HIS D 269 PHE 0.029 0.001 PHE D 350 TYR 0.022 0.002 TYR C 504 ARG 0.012 0.001 ARG A 675 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3737.66 seconds wall clock time: 68 minutes 10.67 seconds (4090.67 seconds total)