Starting phenix.real_space_refine on Sun Nov 19 21:38:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/11_2023/7rz7_24753_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/11_2023/7rz7_24753.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/11_2023/7rz7_24753_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/11_2023/7rz7_24753_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/11_2023/7rz7_24753_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/11_2023/7rz7_24753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/11_2023/7rz7_24753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/11_2023/7rz7_24753_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/11_2023/7rz7_24753_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 18046 2.51 5 N 4632 2.21 5 O 5234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ARG 485": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D ARG 485": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 28054 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7823 Classifications: {'peptide': 993} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 965} Chain breaks: 3 Chain: "B" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6178 Classifications: {'peptide': 784} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 760} Chain breaks: 2 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7823 Classifications: {'peptide': 993} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 965} Chain breaks: 3 Chain: "D" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6178 Classifications: {'peptide': 784} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 760} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.43, per 1000 atoms: 0.48 Number of scatterers: 28054 At special positions: 0 Unit cell: (122.935, 161.419, 189.213, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 5234 8.00 N 4632 7.00 C 18046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.06 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.06 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.13 Conformation dependent library (CDL) restraints added in 4.4 seconds 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 22 sheets defined 44.3% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.500A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 4.169A pdb=" N LYS A 173 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ASP A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR A 177 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG A 178 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 180 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 181 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 182 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.707A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 517 through 520 Proline residue: A 520 - end of helix No H-bonds generated for 'chain 'A' and resid 517 through 520' Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.607A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.570A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 629 removed outlier: 3.572A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 641 No H-bonds generated for 'chain 'A' and resid 638 through 641' Processing helix chain 'A' and resid 655 through 660 Processing helix chain 'A' and resid 665 through 674 removed outlier: 3.816A pdb=" N MET A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.831A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.536A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 758 through 768 removed outlier: 5.042A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 820 removed outlier: 3.929A pdb=" N ALA A 793 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLY A 794 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 795 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 798 " --> pdb=" O VAL A 795 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 800 " --> pdb=" O TYR A 797 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY A 804 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 807 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 808 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU A 813 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 815 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 817 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 818 " --> pdb=" O CYS A 815 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 819 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 857 removed outlier: 3.806A pdb=" N LEU A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 917 through 951 removed outlier: 3.574A pdb=" N MET A 924 " --> pdb=" O ASN A 920 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 928 " --> pdb=" O MET A 924 " (cutoff:3.500A) Proline residue: A 930 - end of helix removed outlier: 3.710A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS A 950 " --> pdb=" O SER A 946 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 951 " --> pdb=" O ASN A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 990 removed outlier: 3.510A pdb=" N ALA A 959 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 961 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY A 963 " --> pdb=" O PHE A 960 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU A 968 " --> pdb=" O PHE A 965 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 970 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 971 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 978 " --> pdb=" O VAL A 975 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 979 " --> pdb=" O GLY A 976 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 981 " --> pdb=" O VAL A 978 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER A 982 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN A 985 " --> pdb=" O SER A 982 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP A 986 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1034 removed outlier: 3.506A pdb=" N PHE A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.885A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.522A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.734A pdb=" N VAL B 82 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN B 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 86 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 87 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS B 89 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.604A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 144 through 155 removed outlier: 4.092A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 186 removed outlier: 3.889A pdb=" N LYS B 173 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASP B 174 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU B 175 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 177 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG B 178 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN B 182 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 185 " --> pdb=" O GLN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.778A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.847A pdb=" N GLU B 330 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 334 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 436 removed outlier: 3.567A pdb=" N LYS B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS B 436 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 483 through 488 removed outlier: 4.134A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 removed outlier: 3.543A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) Proline residue: B 520 - end of helix No H-bonds generated for 'chain 'B' and resid 516 through 520' Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.540A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 removed outlier: 3.582A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 625 removed outlier: 3.592A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.515A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 641' Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.652A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 removed outlier: 3.679A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 694 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.594A pdb=" N ILE B 712 " --> pdb=" O MET B 708 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 removed outlier: 3.737A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 775 through 779 Processing helix chain 'B' and resid 793 through 817 removed outlier: 3.506A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 144 through 156 removed outlier: 3.500A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 4.170A pdb=" N LYS C 173 " --> pdb=" O ASN C 170 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ASP C 174 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 175 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR C 177 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG C 178 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 180 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE C 181 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN C 182 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.501A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.707A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 517 through 520 Proline residue: C 520 - end of helix No H-bonds generated for 'chain 'C' and resid 517 through 520' Processing helix chain 'C' and resid 523 through 544 removed outlier: 3.608A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.570A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 629 removed outlier: 3.572A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 641 No H-bonds generated for 'chain 'C' and resid 638 through 641' Processing helix chain 'C' and resid 655 through 660 Processing helix chain 'C' and resid 665 through 674 removed outlier: 3.817A pdb=" N MET C 670 " --> pdb=" O VAL C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 696 removed outlier: 3.831A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.537A pdb=" N ILE C 712 " --> pdb=" O MET C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 754 Processing helix chain 'C' and resid 758 through 768 removed outlier: 5.042A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 820 removed outlier: 3.929A pdb=" N ALA C 793 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLY C 794 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 795 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 798 " --> pdb=" O VAL C 795 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL C 800 " --> pdb=" O TYR C 797 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY C 804 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C 807 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 808 " --> pdb=" O LEU C 805 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU C 813 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS C 815 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 817 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER C 818 " --> pdb=" O CYS C 815 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 819 " --> pdb=" O TYR C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 857 removed outlier: 3.805A pdb=" N LEU C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 841 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 896 No H-bonds generated for 'chain 'C' and resid 894 through 896' Processing helix chain 'C' and resid 917 through 951 removed outlier: 3.574A pdb=" N MET C 924 " --> pdb=" O ASN C 920 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA C 928 " --> pdb=" O MET C 924 " (cutoff:3.500A) Proline residue: C 930 - end of helix removed outlier: 3.708A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 937 " --> pdb=" O LEU C 933 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET C 939 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 944 " --> pdb=" O PHE C 940 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 945 " --> pdb=" O ILE C 941 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 948 " --> pdb=" O ILE C 944 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS C 950 " --> pdb=" O SER C 946 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE C 951 " --> pdb=" O ASN C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 990 removed outlier: 3.510A pdb=" N ALA C 959 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 961 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY C 963 " --> pdb=" O PHE C 960 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU C 968 " --> pdb=" O PHE C 965 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 970 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 971 " --> pdb=" O LEU C 968 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 978 " --> pdb=" O VAL C 975 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 979 " --> pdb=" O GLY C 976 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 981 " --> pdb=" O VAL C 978 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER C 982 " --> pdb=" O LEU C 979 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN C 985 " --> pdb=" O SER C 982 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP C 986 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1034 removed outlier: 3.506A pdb=" N PHE C1014 " --> pdb=" O ALA C1010 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 3.884A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.523A pdb=" N ALA D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.734A pdb=" N VAL D 82 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN D 83 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 86 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS D 89 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.604A pdb=" N ILE D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 144 through 155 removed outlier: 4.093A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 186 removed outlier: 3.889A pdb=" N LYS D 173 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASP D 174 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 175 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR D 177 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG D 178 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 185 " --> pdb=" O GLN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.777A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 removed outlier: 3.848A pdb=" N GLU D 330 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG D 331 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS D 334 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 434 removed outlier: 3.568A pdb=" N LYS D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 467 Processing helix chain 'D' and resid 483 through 488 removed outlier: 4.133A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 520 removed outlier: 3.543A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) Proline residue: D 520 - end of helix No H-bonds generated for 'chain 'D' and resid 516 through 520' Processing helix chain 'D' and resid 523 through 546 removed outlier: 3.540A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 584 removed outlier: 3.582A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 removed outlier: 3.592A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 641 removed outlier: 3.515A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 637 through 641' Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.651A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.679A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 694 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.593A pdb=" N ILE D 712 " --> pdb=" O MET D 708 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 755 removed outlier: 3.736A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 753 " --> pdb=" O ALA D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 775 through 779 Processing helix chain 'D' and resid 793 through 817 removed outlier: 3.507A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS D 815 " --> pdb=" O LEU D 811 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 50 removed outlier: 6.987A pdb=" N ALA A 72 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU A 17 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE A 74 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 95 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY A 75 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE A 97 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.064A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= D, first strand: chain 'A' and resid 720 through 723 removed outlier: 3.508A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 999 through 1003 removed outlier: 3.861A pdb=" N LEU A 862 " --> pdb=" O SER A 884 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE A 868 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL A 878 " --> pdb=" O ILE A 868 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 888 through 890 Processing sheet with id= G, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.246A pdb=" N ARG B 42 " --> pdb=" O ILE B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.141A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER B 95 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLY B 75 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE B 97 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.096A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS B 364 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 397 through 399 removed outlier: 3.913A pdb=" N THR B 399 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.439A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.987A pdb=" N ALA C 72 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU C 17 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE C 74 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER C 95 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY C 75 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE C 97 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.064A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= O, first strand: chain 'C' and resid 720 through 723 removed outlier: 3.509A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 999 through 1003 removed outlier: 3.861A pdb=" N LEU C 862 " --> pdb=" O SER C 884 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE C 868 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL C 878 " --> pdb=" O ILE C 868 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 888 through 890 Processing sheet with id= R, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.246A pdb=" N ARG D 42 " --> pdb=" O ILE D 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.141A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER D 95 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLY D 75 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE D 97 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.096A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS D 364 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 397 through 399 removed outlier: 3.913A pdb=" N THR D 399 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.439A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 1028 hydrogen bonds defined for protein. 2706 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.12 Time building geometry restraints manager: 11.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8838 1.34 - 1.46: 7046 1.46 - 1.58: 12532 1.58 - 1.70: 4 1.70 - 1.82: 232 Bond restraints: 28652 Sorted by residual: bond pdb=" C05 QUS B1301 " pdb=" O19 QUS B1301 " ideal model delta sigma weight residual 1.185 1.449 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C05 QUS D1301 " pdb=" O19 QUS D1301 " ideal model delta sigma weight residual 1.185 1.448 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C05 QUS A1301 " pdb=" O19 QUS A1301 " ideal model delta sigma weight residual 1.185 1.448 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C05 QUS C1301 " pdb=" O19 QUS C1301 " ideal model delta sigma weight residual 1.185 1.447 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C04 QUS D1301 " pdb=" O18 QUS D1301 " ideal model delta sigma weight residual 1.185 1.413 -0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 28647 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.22: 424 105.22 - 112.54: 14439 112.54 - 119.85: 10164 119.85 - 127.17: 13440 127.17 - 134.48: 247 Bond angle restraints: 38714 Sorted by residual: angle pdb=" CA LEU C 43 " pdb=" CB LEU C 43 " pdb=" CG LEU C 43 " ideal model delta sigma weight residual 116.30 134.48 -18.18 3.50e+00 8.16e-02 2.70e+01 angle pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sigma weight residual 116.30 134.44 -18.14 3.50e+00 8.16e-02 2.69e+01 angle pdb=" C LYS A 716 " pdb=" N PRO A 717 " pdb=" CA PRO A 717 " ideal model delta sigma weight residual 119.84 113.68 6.16 1.25e+00 6.40e-01 2.43e+01 angle pdb=" C LYS C 716 " pdb=" N PRO C 717 " pdb=" CA PRO C 717 " ideal model delta sigma weight residual 119.84 113.68 6.16 1.25e+00 6.40e-01 2.42e+01 angle pdb=" C ASP C 378 " pdb=" N LYS C 379 " pdb=" CA LYS C 379 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 ... (remaining 38709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16123 17.92 - 35.83: 678 35.83 - 53.75: 150 53.75 - 71.67: 17 71.67 - 89.58: 4 Dihedral angle restraints: 16972 sinusoidal: 6742 harmonic: 10230 Sorted by residual: dihedral pdb=" CA LYS D 716 " pdb=" C LYS D 716 " pdb=" N PRO D 717 " pdb=" CA PRO D 717 " ideal model delta harmonic sigma weight residual 180.00 138.11 41.89 0 5.00e+00 4.00e-02 7.02e+01 dihedral pdb=" CA LYS B 716 " pdb=" C LYS B 716 " pdb=" N PRO B 717 " pdb=" CA PRO B 717 " ideal model delta harmonic sigma weight residual 180.00 138.14 41.86 0 5.00e+00 4.00e-02 7.01e+01 dihedral pdb=" CA ASP C 378 " pdb=" C ASP C 378 " pdb=" N LYS C 379 " pdb=" CA LYS C 379 " ideal model delta harmonic sigma weight residual 180.00 -139.91 -40.09 0 5.00e+00 4.00e-02 6.43e+01 ... (remaining 16969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3851 0.083 - 0.167: 419 0.167 - 0.250: 28 0.250 - 0.334: 4 0.334 - 0.417: 2 Chirality restraints: 4304 Sorted by residual: chirality pdb=" CG LEU C 892 " pdb=" CB LEU C 892 " pdb=" CD1 LEU C 892 " pdb=" CD2 LEU C 892 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CG LEU A 892 " pdb=" CB LEU A 892 " pdb=" CD1 LEU A 892 " pdb=" CD2 LEU A 892 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CG LEU C 989 " pdb=" CB LEU C 989 " pdb=" CD1 LEU C 989 " pdb=" CD2 LEU C 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4301 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 716 " 0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO A 717 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO C 717 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 716 " -0.058 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO D 717 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 717 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 717 " -0.049 5.00e-02 4.00e+02 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7165 2.78 - 3.31: 25534 3.31 - 3.84: 46333 3.84 - 4.37: 54736 4.37 - 4.90: 89975 Nonbonded interactions: 223743 Sorted by model distance: nonbonded pdb=" O MET A 33 " pdb=" OG SER A 37 " model vdw 2.256 2.440 nonbonded pdb=" O MET C 33 " pdb=" OG SER C 37 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR B 135 " pdb=" OD2 ASP B 195 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR D 135 " pdb=" OD2 ASP D 195 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR A 38 " pdb=" O PHE A 41 " model vdw 2.296 2.440 ... (remaining 223738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 11.700 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 66.910 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.007 0.264 28652 Z= 0.484 Angle : 0.926 18.182 38714 Z= 0.505 Chirality : 0.054 0.417 4304 Planarity : 0.007 0.113 4878 Dihedral : 10.901 89.583 10410 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 0.66 % Allowed : 5.34 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -4.36 (0.11), residues: 3526 helix: -3.39 (0.07), residues: 1612 sheet: -1.88 (0.22), residues: 450 loop : -2.40 (0.14), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 659 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 3 residues processed: 678 average time/residue: 0.4169 time to fit residues: 440.7781 Evaluate side-chains 350 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 347 time to evaluate : 3.175 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2386 time to fit residues: 5.7066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.0470 chunk 268 optimal weight: 0.2980 chunk 148 optimal weight: 0.0170 chunk 91 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 277 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 overall best weight: 1.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 214 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 587 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS B 219 HIS B 355 ASN B 359 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS C 214 HIS ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS D 355 ASN D 359 ASN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28652 Z= 0.187 Angle : 0.585 8.568 38714 Z= 0.313 Chirality : 0.042 0.247 4304 Planarity : 0.005 0.080 4878 Dihedral : 6.422 85.889 3862 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.59 (0.12), residues: 3526 helix: -1.33 (0.11), residues: 1674 sheet: -1.66 (0.23), residues: 440 loop : -2.06 (0.14), residues: 1412 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 488 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 489 average time/residue: 0.4058 time to fit residues: 316.2441 Evaluate side-chains 326 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 3.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 322 optimal weight: 7.9990 chunk 347 optimal weight: 0.9990 chunk 286 optimal weight: 6.9990 chunk 319 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 219 HIS D 435 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28652 Z= 0.348 Angle : 0.678 9.718 38714 Z= 0.357 Chirality : 0.045 0.194 4304 Planarity : 0.005 0.081 4878 Dihedral : 6.496 81.014 3862 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.13 % Allowed : 3.27 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.74 (0.13), residues: 3526 helix: -0.40 (0.12), residues: 1662 sheet: -1.76 (0.25), residues: 406 loop : -1.77 (0.15), residues: 1458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 398 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 402 average time/residue: 0.3748 time to fit residues: 243.3523 Evaluate side-chains 299 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 296 time to evaluate : 2.911 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2289 time to fit residues: 5.3845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 8.9990 chunk 242 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 chunk 323 optimal weight: 0.8980 chunk 342 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 355 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 435 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28652 Z= 0.213 Angle : 0.563 8.296 38714 Z= 0.295 Chirality : 0.042 0.224 4304 Planarity : 0.004 0.069 4878 Dihedral : 6.041 83.058 3862 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.29 (0.14), residues: 3526 helix: 0.11 (0.13), residues: 1672 sheet: -1.67 (0.25), residues: 416 loop : -1.68 (0.15), residues: 1438 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 401 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 402 average time/residue: 0.3869 time to fit residues: 254.0014 Evaluate side-chains 282 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.102 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 291 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN D 435 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28652 Z= 0.243 Angle : 0.581 10.632 38714 Z= 0.302 Chirality : 0.042 0.323 4304 Planarity : 0.004 0.070 4878 Dihedral : 5.951 83.624 3862 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3526 helix: 0.28 (0.13), residues: 1684 sheet: -1.69 (0.25), residues: 414 loop : -1.62 (0.16), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 380 time to evaluate : 3.131 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: 1 outliers final: 0 residues processed: 381 average time/residue: 0.4133 time to fit residues: 260.0618 Evaluate side-chains 290 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 3.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 0.7980 chunk 308 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 342 optimal weight: 9.9990 chunk 284 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN D 435 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28652 Z= 0.225 Angle : 0.567 9.667 38714 Z= 0.294 Chirality : 0.042 0.225 4304 Planarity : 0.004 0.068 4878 Dihedral : 5.852 83.207 3862 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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 (0.14), residues: 3526 helix: 0.39 (0.13), residues: 1684 sheet: -1.69 (0.26), residues: 390 loop : -1.62 (0.15), residues: 1452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3687 time to fit residues: 219.0647 Evaluate side-chains 277 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 2.986 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 250 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 341 optimal weight: 0.4980 chunk 213 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN B 355 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28652 Z= 0.156 Angle : 0.540 11.496 38714 Z= 0.277 Chirality : 0.041 0.203 4304 Planarity : 0.004 0.070 4878 Dihedral : 5.630 84.004 3862 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.78 (0.14), residues: 3526 helix: 0.66 (0.13), residues: 1666 sheet: -1.75 (0.25), residues: 402 loop : -1.49 (0.16), residues: 1458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.3685 time to fit residues: 228.6227 Evaluate side-chains 284 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 3.436 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 3.9990 chunk 136 optimal weight: 0.0070 chunk 203 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 0.0170 chunk 31 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28652 Z= 0.172 Angle : 0.547 11.840 38714 Z= 0.280 Chirality : 0.041 0.200 4304 Planarity : 0.004 0.068 4878 Dihedral : 5.556 87.173 3862 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.71 (0.14), residues: 3526 helix: 0.72 (0.13), residues: 1662 sheet: -1.70 (0.25), residues: 404 loop : -1.46 (0.16), residues: 1460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.3710 time to fit residues: 220.1215 Evaluate side-chains 285 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 3.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 chunk 317 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 chunk 300 optimal weight: 4.9990 chunk 316 optimal weight: 0.0270 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28652 Z= 0.144 Angle : 0.535 11.891 38714 Z= 0.273 Chirality : 0.041 0.192 4304 Planarity : 0.004 0.069 4878 Dihedral : 5.457 88.679 3862 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.62 (0.14), residues: 3526 helix: 0.81 (0.13), residues: 1664 sheet: -1.63 (0.26), residues: 400 loop : -1.45 (0.15), residues: 1462 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.3909 time to fit residues: 242.7849 Evaluate side-chains 291 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 3.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 0.0060 chunk 336 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 chunk 352 optimal weight: 4.9990 chunk 324 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28652 Z= 0.181 Angle : 0.558 11.588 38714 Z= 0.284 Chirality : 0.041 0.190 4304 Planarity : 0.004 0.069 4878 Dihedral : 5.448 87.870 3862 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3526 helix: 0.89 (0.13), residues: 1642 sheet: -1.64 (0.26), residues: 400 loop : -1.47 (0.15), residues: 1484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 3.273 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: 0 outliers final: 0 residues processed: 352 average time/residue: 0.3606 time to fit residues: 213.1393 Evaluate side-chains 279 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 3.032 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 9.9990 chunk 299 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 258 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 281 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** 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 = 0.3775 r_free = 0.3775 target = 0.101505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075110 restraints weight = 98802.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.074862 restraints weight = 62589.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.075460 restraints weight = 42816.381| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28652 Z= 0.148 Angle : 0.538 11.545 38714 Z= 0.273 Chirality : 0.041 0.186 4304 Planarity : 0.004 0.068 4878 Dihedral : 5.344 88.887 3862 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.52 (0.14), residues: 3526 helix: 0.94 (0.13), residues: 1654 sheet: -1.58 (0.26), residues: 400 loop : -1.46 (0.15), residues: 1472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5684.02 seconds wall clock time: 105 minutes 5.10 seconds (6305.10 seconds total)