Starting phenix.real_space_refine (version: dev) on Fri Apr 8 08:08:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/04_2022/3jbx_6487.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/04_2022/3jbx_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_6487/04_2022/3jbx_6487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/04_2022/3jbx_6487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/04_2022/3jbx_6487.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/04_2022/3jbx_6487.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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-4553/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: {'PTRANS': 19, 'CIS': 4, 'TRANS': 524, 'PCIS': 2} Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 22, 'CIS': 8, 'TRANS': 318, 'PCIS': 2} Chain: "C" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4435 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 19, 'CIS': 4, 'TRANS': 524, 'PCIS': 2} Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 22, 'CIS': 9, 'TRANS': 317, 'PCIS': 2} 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: {' ZN': 1, ' MG': 2} 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: {' ZN': 1, ' MG': 2} 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: 9.97, per 1000 atoms: 0.60 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: 7.70 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 5.37 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: 7.10 Time building geometry restraints manager: 8.15 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: 8910 28.74 - 57.48: 972 57.48 - 86.22: 99 86.22 - 114.96: 5 114.96 - 143.70: 2 Dihedral angle restraints: 9988 sinusoidal: 4776 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 9985 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 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. 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.010 Extract box with map and model: 3.120 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.130 Process input model: 54.420 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 1.236 13.563 23828 Z= 0.825 Chirality : 0.049 0.414 2600 Planarity : 0.014 0.468 2682 Dihedral : 21.133 143.696 6636 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 % 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 *********************** 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 : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 186 outliers final: 41 residues processed: 593 average time/residue: 0.3017 time to fit residues: 261.3638 Evaluate side-chains 300 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 259 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1652 time to fit residues: 14.8707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN A1000 GLN B 4 GLN B 64 ASN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 822 ASN C 858 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 17268 Z= 0.346 Angle : 0.830 20.600 23828 Z= 0.434 Chirality : 0.047 0.259 2600 Planarity : 0.006 0.083 2682 Dihedral : 22.128 151.424 3118 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.90 % Favored : 96.99 % Rotamer Outliers : 5.37 % 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: -1.84 (0.17), residues: 1794 helix: -0.87 (0.20), residues: 544 sheet: -0.26 (0.27), residues: 284 loop : -1.74 (0.17), residues: 966 *********************** 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 379 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 294 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 46 residues processed: 355 average time/residue: 0.2979 time to fit residues: 158.1260 Evaluate side-chains 280 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 234 time to evaluate : 1.806 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.1663 time to fit residues: 16.2818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS B 65 ASN B 204 GLN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 17268 Z= 0.316 Angle : 0.759 17.165 23828 Z= 0.398 Chirality : 0.044 0.228 2600 Planarity : 0.006 0.091 2682 Dihedral : 22.192 149.993 3118 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.35 % Favored : 95.54 % Rotamer Outliers : 2.65 % 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: -1.33 (0.18), residues: 1794 helix: -0.27 (0.21), residues: 544 sheet: -0.20 (0.27), residues: 318 loop : -1.50 (0.18), residues: 932 *********************** 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 318 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 276 time to evaluate : 2.019 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 14 residues processed: 306 average time/residue: 0.3139 time to fit residues: 142.9237 Evaluate side-chains 250 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 236 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1705 time to fit residues: 6.9571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 146 ASN C 492 ASN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 17268 Z= 0.322 Angle : 0.741 16.187 23828 Z= 0.386 Chirality : 0.044 0.201 2600 Planarity : 0.006 0.092 2682 Dihedral : 22.301 151.474 3118 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % Rotamer Outliers : 3.85 % 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: -1.17 (0.18), residues: 1794 helix: -0.08 (0.21), residues: 548 sheet: -0.16 (0.27), residues: 330 loop : -1.44 (0.18), residues: 916 *********************** 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 320 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 259 time to evaluate : 1.845 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 29 residues processed: 294 average time/residue: 0.2930 time to fit residues: 130.7177 Evaluate side-chains 253 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1832 time to fit residues: 11.8068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 125 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN B 204 GLN C 492 ASN C 517 GLN C 956 ASN D 10 ASN D 117 ASN D 298 HIS ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 17268 Z= 0.204 Angle : 0.689 15.870 23828 Z= 0.358 Chirality : 0.041 0.211 2600 Planarity : 0.005 0.084 2682 Dihedral : 22.085 154.990 3118 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer Outliers : 2.53 % 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: -0.86 (0.19), residues: 1794 helix: 0.28 (0.22), residues: 534 sheet: -0.01 (0.28), residues: 328 loop : -1.28 (0.19), residues: 932 *********************** 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 308 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 268 time to evaluate : 1.820 Fit side-chains outliers start: 40 outliers final: 14 residues processed: 300 average time/residue: 0.2752 time to fit residues: 126.7347 Evaluate side-chains 252 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 238 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1852 time to fit residues: 7.0113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN B 65 ASN B 170 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C1028 HIS D 298 HIS ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.098 17268 Z= 0.363 Angle : 0.744 15.822 23828 Z= 0.385 Chirality : 0.044 0.214 2600 Planarity : 0.006 0.086 2682 Dihedral : 22.244 156.631 3118 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.35 % Favored : 95.54 % Rotamer Outliers : 2.71 % 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: -0.90 (0.19), residues: 1794 helix: 0.25 (0.22), residues: 544 sheet: -0.04 (0.28), residues: 328 loop : -1.33 (0.19), residues: 922 *********************** 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 300 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 257 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 286 average time/residue: 0.2817 time to fit residues: 123.5646 Evaluate side-chains 252 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 1.925 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2006 time to fit residues: 9.5679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN B 170 GLN B 269 HIS C 492 ASN D 298 HIS ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 17268 Z= 0.323 Angle : 0.732 15.713 23828 Z= 0.377 Chirality : 0.043 0.208 2600 Planarity : 0.006 0.077 2682 Dihedral : 22.225 157.151 3118 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.85 % Favored : 95.04 % Rotamer Outliers : 1.70 % 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: -0.91 (0.19), residues: 1794 helix: 0.20 (0.22), residues: 546 sheet: 0.04 (0.28), residues: 328 loop : -1.33 (0.19), residues: 920 *********************** 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 275 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 248 time to evaluate : 1.949 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 7 residues processed: 268 average time/residue: 0.3073 time to fit residues: 124.2496 Evaluate side-chains 248 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 241 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1626 time to fit residues: 4.6180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 822 ASN D 298 HIS ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.113 17268 Z= 0.221 Angle : 0.693 15.589 23828 Z= 0.357 Chirality : 0.041 0.204 2600 Planarity : 0.006 0.087 2682 Dihedral : 22.059 156.559 3118 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % Rotamer Outliers : 0.76 % 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: -0.72 (0.19), residues: 1794 helix: 0.42 (0.22), residues: 544 sheet: 0.12 (0.28), residues: 328 loop : -1.26 (0.19), residues: 922 *********************** 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 274 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 262 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 271 average time/residue: 0.2779 time to fit residues: 115.8540 Evaluate side-chains 245 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1545 time to fit residues: 3.6295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 0.3980 chunk 132 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN D 298 HIS ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.134 17268 Z= 0.240 Angle : 0.707 15.479 23828 Z= 0.366 Chirality : 0.042 0.206 2600 Planarity : 0.006 0.115 2682 Dihedral : 21.998 156.501 3118 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.60 % Rotamer Outliers : 0.88 % 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: -0.66 (0.19), residues: 1794 helix: 0.52 (0.22), residues: 540 sheet: 0.12 (0.28), residues: 348 loop : -1.26 (0.20), residues: 906 *********************** 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 269 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 255 time to evaluate : 1.905 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 263 average time/residue: 0.2852 time to fit residues: 116.1318 Evaluate side-chains 251 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 245 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1652 time to fit residues: 4.2146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.147 17268 Z= 0.364 Angle : 0.760 15.506 23828 Z= 0.397 Chirality : 0.044 0.210 2600 Planarity : 0.007 0.149 2682 Dihedral : 22.185 156.484 3118 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.37 % Rotamer Outliers : 0.63 % 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: -0.81 (0.19), residues: 1794 helix: 0.40 (0.22), residues: 540 sheet: 0.03 (0.27), residues: 350 loop : -1.35 (0.20), residues: 904 ********************** 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 245 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 1.852 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 242 average time/residue: 0.2915 time to fit residues: 108.4743 Evaluate side-chains 235 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 230 time to evaluate : 2.006 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1877 time to fit residues: 4.3782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 131 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS ** D 313 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 = 0.3834 r_free = 0.3834 target = 0.139963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115328 restraints weight = 26849.465| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.34 r_work: 0.3484 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work: 0.3459 rms_B_bonded: 2.17 restraints_weight: 0.1250 r_work: 0.3445 rms_B_bonded: 2.28 restraints_weight: 0.0625 r_work: 0.3431 rms_B_bonded: 2.42 restraints_weight: 0.0312 r_work: 0.3416 rms_B_bonded: 2.61 restraints_weight: 0.0156 r_work: 0.3399 rms_B_bonded: 2.83 restraints_weight: 0.0078 r_work: 0.3382 rms_B_bonded: 3.10 restraints_weight: 0.0039 r_work: 0.3362 rms_B_bonded: 3.42 restraints_weight: 0.0020 r_work: 0.3341 rms_B_bonded: 3.78 restraints_weight: 0.0010 r_work: 0.3318 rms_B_bonded: 4.21 restraints_weight: 0.0005 r_work: 0.3293 rms_B_bonded: 4.70 restraints_weight: 0.0002 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.141 17268 Z= 0.220 Angle : 0.710 15.334 23828 Z= 0.365 Chirality : 0.041 0.204 2600 Planarity : 0.007 0.128 2682 Dihedral : 22.081 156.534 3118 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.35 % Favored : 95.54 % Rotamer Outliers : 0.63 % 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: -0.65 (0.19), residues: 1794 helix: 0.59 (0.22), residues: 536 sheet: 0.11 (0.28), residues: 348 loop : -1.28 (0.20), residues: 910 =============================================================================== Job complete usr+sys time: 3327.87 seconds wall clock time: 61 minutes 37.77 seconds (3697.77 seconds total)