Starting phenix.real_space_refine (version: dev) on Sun Dec 18 16:22:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/12_2022/3jbx_6487.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/12_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_6487/12_2022/3jbx_6487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/12_2022/3jbx_6487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/12_2022/3jbx_6487.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jbx_6487/12_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 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 9.63, per 1000 atoms: 0.58 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: 7.56 Conformation dependent library (CDL) restraints added in 2.0 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: 5.74 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: 7.63 Time building geometry restraints manager: 8.16 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: 0.340 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: 3.170 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.140 Process input model: 54.840 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.820 ------------------------------------------------------------------------------- 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 : 16.87 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 : 1.890 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: 0.3039 time to fit residues: 262.9428 Evaluate side-chains 302 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 261 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1680 time to fit residues: 15.1083 ------------------------------------------------------------------------------- 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: 3.9990 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: 2.3786 ------------------------------------------------------------------------------- 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 170 GLN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 17268 Z= 0.324 Angle : 0.822 19.678 23828 Z= 0.430 Chirality : 0.046 0.225 2600 Planarity : 0.006 0.066 2682 Dihedral : 22.063 151.069 3118 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.01 % Favored : 96.88 % Rotamer Outliers : 4.86 % 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: -1.83 (0.17), residues: 1794 helix: -0.88 (0.20), residues: 546 sheet: -0.34 (0.26), residues: 294 loop : -1.70 (0.17), residues: 954 *********************** 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 371 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 294 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 40 residues processed: 349 average time/residue: 0.3077 time to fit residues: 160.4559 Evaluate side-chains 281 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 241 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.1626 time to fit residues: 14.2414 ------------------------------------------------------------------------------- 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: 9.9990 chunk 52 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS A 629 HIS B 65 ASN B 170 GLN B 204 GLN C 517 GLN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 17268 Z= 0.232 Angle : 0.720 16.406 23828 Z= 0.375 Chirality : 0.043 0.197 2600 Planarity : 0.005 0.079 2682 Dihedral : 22.093 150.464 3118 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.76 % Rotamer Outliers : 3.16 % 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: -1.20 (0.18), residues: 1794 helix: -0.11 (0.21), residues: 548 sheet: -0.19 (0.26), residues: 342 loop : -1.46 (0.18), residues: 904 *********************** 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 331 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 281 time to evaluate : 1.911 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 18 residues processed: 313 average time/residue: 0.2995 time to fit residues: 138.3805 Evaluate side-chains 254 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 1.749 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1917 time to fit residues: 8.3750 ------------------------------------------------------------------------------- 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: 7.9990 chunk 128 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 65 ASN B 146 ASN B 170 GLN B 204 GLN C 492 ASN C 822 ASN ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 17268 Z= 0.306 Angle : 0.725 16.264 23828 Z= 0.377 Chirality : 0.043 0.206 2600 Planarity : 0.006 0.076 2682 Dihedral : 22.206 151.597 3118 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.79 % Favored : 96.10 % Rotamer Outliers : 3.09 % 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: -1.03 (0.18), residues: 1794 helix: 0.07 (0.21), residues: 546 sheet: -0.18 (0.27), residues: 350 loop : -1.35 (0.19), residues: 898 *********************** 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 306 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 257 time to evaluate : 1.834 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 290 average time/residue: 0.2672 time to fit residues: 118.4028 Evaluate side-chains 269 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 1.837 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1548 time to fit residues: 9.3222 ------------------------------------------------------------------------------- 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: 3.9990 chunk 103 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN B 204 GLN C 492 ASN C 956 ASN D 117 ASN 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: 0.8246 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 17268 Z= 0.220 Angle : 0.684 15.944 23828 Z= 0.356 Chirality : 0.041 0.198 2600 Planarity : 0.005 0.073 2682 Dihedral : 22.039 155.023 3118 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % 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: -0.86 (0.19), residues: 1794 helix: 0.30 (0.22), residues: 544 sheet: -0.06 (0.27), residues: 346 loop : -1.32 (0.19), residues: 904 *********************** 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 316 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 274 time to evaluate : 2.066 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 14 residues processed: 306 average time/residue: 0.2803 time to fit residues: 130.3971 Evaluate side-chains 246 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 232 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2235 time to fit residues: 7.4414 ------------------------------------------------------------------------------- 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: 0.0970 chunk 163 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 150 optimal weight: 0.4980 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 170 GLN B 298 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: 0.8226 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 17268 Z= 0.205 Angle : 0.680 14.620 23828 Z= 0.350 Chirality : 0.041 0.204 2600 Planarity : 0.005 0.072 2682 Dihedral : 22.030 157.251 3118 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.62 % Favored : 96.27 % Rotamer Outliers : 2.21 % 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: -0.73 (0.19), residues: 1794 helix: 0.37 (0.22), residues: 544 sheet: 0.01 (0.27), residues: 352 loop : -1.20 (0.19), residues: 898 *********************** 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 308 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 273 time to evaluate : 1.828 Fit side-chains outliers start: 35 outliers final: 13 residues processed: 293 average time/residue: 0.2834 time to fit residues: 126.1535 Evaluate side-chains 268 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 255 time to evaluate : 1.831 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1553 time to fit residues: 6.1398 ------------------------------------------------------------------------------- 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: 20.0000 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 0.0770 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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 298 HIS C 492 ASN C1028 HIS 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: 0.8271 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 17268 Z= 0.277 Angle : 0.704 14.779 23828 Z= 0.363 Chirality : 0.042 0.204 2600 Planarity : 0.005 0.073 2682 Dihedral : 22.092 156.739 3118 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.90 % Favored : 95.99 % Rotamer Outliers : 1.96 % 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: -0.74 (0.19), residues: 1794 helix: 0.35 (0.22), residues: 544 sheet: -0.01 (0.27), residues: 358 loop : -1.21 (0.20), residues: 892 *********************** 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 288 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 257 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 276 average time/residue: 0.2732 time to fit residues: 115.8293 Evaluate side-chains 262 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 244 time to evaluate : 1.881 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1710 time to fit residues: 8.0010 ------------------------------------------------------------------------------- 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: 0.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 115 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 170 GLN B 298 HIS C 492 ASN D 269 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: 0.8233 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 17268 Z= 0.216 Angle : 0.687 14.526 23828 Z= 0.353 Chirality : 0.041 0.201 2600 Planarity : 0.005 0.071 2682 Dihedral : 22.003 156.323 3118 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.35 % Favored : 95.54 % Rotamer Outliers : 1.07 % 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: 0.47 (0.22), residues: 544 sheet: 0.12 (0.27), residues: 348 loop : -1.20 (0.20), residues: 902 *********************** 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 279 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 262 time to evaluate : 2.061 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 276 average time/residue: 0.2773 time to fit residues: 117.5270 Evaluate side-chains 250 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 1.879 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1554 time to fit residues: 4.1944 ------------------------------------------------------------------------------- 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: 0.6980 chunk 158 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 17268 Z= 0.222 Angle : 0.692 15.225 23828 Z= 0.356 Chirality : 0.041 0.202 2600 Planarity : 0.005 0.071 2682 Dihedral : 21.900 156.155 3118 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.46 % Favored : 95.43 % Rotamer Outliers : 0.82 % 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: -0.60 (0.19), residues: 1794 helix: 0.48 (0.22), residues: 546 sheet: 0.19 (0.27), residues: 346 loop : -1.18 (0.20), residues: 902 *********************** 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 275 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 262 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 269 average time/residue: 0.2818 time to fit residues: 115.5327 Evaluate side-chains 251 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 244 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2346 time to fit residues: 5.0274 ------------------------------------------------------------------------------- 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: 0.0470 chunk 84 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 298 HIS 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: 0.8219 moved from start: 0.5036 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= 0.214 Angle : 0.697 14.418 23828 Z= 0.357 Chirality : 0.041 0.202 2600 Planarity : 0.006 0.144 2682 Dihedral : 21.852 155.892 3118 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.46 % Favored : 95.43 % Rotamer Outliers : 0.25 % 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: -0.55 (0.19), residues: 1794 helix: 0.50 (0.22), residues: 546 sheet: 0.21 (0.27), residues: 346 loop : -1.14 (0.20), residues: 902 ********************** 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 266 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 262 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 264 average time/residue: 0.2897 time to fit residues: 116.8390 Evaluate side-chains 246 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4104 ------------------------------------------------------------------------------- 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: 3.9990 chunk 137 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 153 optimal weight: 0.0670 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 overall best weight: 1.4322 ------------------------------------------------------------------------------- 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 298 HIS ** 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 = 0.3836 r_free = 0.3836 target = 0.140146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114829 restraints weight = 26810.334| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.39 r_work: 0.3362 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 17268 Z= 0.227 Angle : 0.700 16.114 23828 Z= 0.359 Chirality : 0.041 0.204 2600 Planarity : 0.005 0.105 2682 Dihedral : 21.829 155.782 3118 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.46 % Favored : 95.43 % Rotamer Outliers : 0.69 % 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: -0.53 (0.19), residues: 1794 helix: 0.53 (0.22), residues: 546 sheet: 0.24 (0.27), residues: 346 loop : -1.14 (0.20), residues: 902 =============================================================================== Job complete usr+sys time: 3361.98 seconds wall clock time: 61 minutes 36.84 seconds (3696.84 seconds total)