Starting phenix.real_space_refine on Tue Feb 20 13:53:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/02_2024/7rz7_24753_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/02_2024/7rz7_24753.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/02_2024/7rz7_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_24753/02_2024/7rz7_24753_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/02_2024/7rz7_24753_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/02_2024/7rz7_24753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/02_2024/7rz7_24753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/02_2024/7rz7_24753_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rz7_24753/02_2024/7rz7_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 14.02, per 1000 atoms: 0.50 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: 10.59 Conformation dependent library (CDL) restraints added in 4.5 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: 6.78 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: 9.77 Time building geometry restraints manager: 11.61 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: 2.710 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: 0.020 Extract box with map and model: 11.560 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 70.880 Find NCS groups from input model: 1.490 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.570 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 374 HIS 0.008 0.002 HIS D 93 PHE 0.022 0.003 PHE D 245 TYR 0.035 0.003 TYR D 218 ARG 0.011 0.001 ARG D 300 *********************** 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 : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 THR cc_start: 0.9382 (m) cc_final: 0.9092 (p) REVERT: A 419 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7676 (mp0) REVERT: A 431 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8420 (tp30) REVERT: A 514 VAL cc_start: 0.8992 (m) cc_final: 0.8722 (t) REVERT: A 614 SER cc_start: 0.9406 (m) cc_final: 0.9083 (p) REVERT: A 770 LYS cc_start: 0.7406 (mmpt) cc_final: 0.7032 (tptt) REVERT: A 797 TYR cc_start: 0.6971 (m-10) cc_final: 0.6462 (t80) REVERT: A 805 LEU cc_start: 0.8702 (tp) cc_final: 0.8294 (pp) REVERT: A 819 ARG cc_start: 0.6162 (mmp80) cc_final: 0.5893 (ttt-90) REVERT: A 880 MET cc_start: 0.4247 (tmm) cc_final: 0.3876 (tmm) REVERT: A 924 MET cc_start: 0.6769 (mmt) cc_final: 0.5943 (tpt) REVERT: A 987 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8222 (tp30) REVERT: B 78 ASP cc_start: 0.9061 (t0) cc_final: 0.8473 (p0) REVERT: B 124 LEU cc_start: 0.9162 (tp) cc_final: 0.8929 (tt) REVERT: B 527 MET cc_start: 0.8004 (mtm) cc_final: 0.7562 (mmt) REVERT: B 649 THR cc_start: 0.6249 (p) cc_final: 0.5843 (m) REVERT: B 657 GLU cc_start: 0.8635 (tp30) cc_final: 0.8171 (mm-30) REVERT: B 803 LEU cc_start: 0.8801 (mt) cc_final: 0.8547 (mt) REVERT: B 811 LEU cc_start: 0.7918 (mm) cc_final: 0.7689 (mp) REVERT: B 817 LYS cc_start: 0.7169 (tptt) cc_final: 0.6643 (ptmm) REVERT: C 43 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7891 (pp) REVERT: C 48 ASP cc_start: 0.8588 (t0) cc_final: 0.8343 (t0) REVERT: C 81 SER cc_start: 0.9102 (p) cc_final: 0.8818 (p) REVERT: C 419 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7687 (mp0) REVERT: C 431 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8623 (tp30) REVERT: C 487 GLU cc_start: 0.7831 (pt0) cc_final: 0.7180 (mp0) REVERT: C 523 TYR cc_start: 0.6666 (p90) cc_final: 0.5509 (t80) REVERT: C 524 GLU cc_start: 0.7994 (mp0) cc_final: 0.7631 (mm-30) REVERT: C 527 MET cc_start: 0.6423 (mmm) cc_final: 0.5791 (mmm) REVERT: C 541 PHE cc_start: 0.7859 (t80) cc_final: 0.7635 (t80) REVERT: C 574 PHE cc_start: 0.8067 (t80) cc_final: 0.7746 (t80) REVERT: C 623 PHE cc_start: 0.8351 (m-10) cc_final: 0.7878 (m-10) REVERT: C 669 LYS cc_start: 0.9012 (tptt) cc_final: 0.8689 (tptp) REVERT: C 798 ILE cc_start: 0.8822 (mt) cc_final: 0.8548 (tp) REVERT: C 883 HIS cc_start: 0.5356 (p90) cc_final: 0.4922 (p90) REVERT: D 330 GLU cc_start: 0.8555 (pt0) cc_final: 0.7952 (pm20) REVERT: D 463 MET cc_start: 0.3822 (mtm) cc_final: 0.3608 (mmp) REVERT: D 527 MET cc_start: 0.8268 (mtm) cc_final: 0.7050 (mmp) REVERT: D 531 PHE cc_start: 0.8225 (m-10) cc_final: 0.8017 (m-10) REVERT: D 534 ILE cc_start: 0.8988 (mt) cc_final: 0.8780 (mm) REVERT: D 540 LEU cc_start: 0.8886 (tt) cc_final: 0.8637 (tt) REVERT: D 649 THR cc_start: 0.6394 (p) cc_final: 0.6033 (m) REVERT: D 673 TYR cc_start: 0.7829 (t80) cc_final: 0.7614 (t80) REVERT: D 693 VAL cc_start: 0.8345 (t) cc_final: 0.7959 (p) REVERT: D 708 MET cc_start: 0.7215 (mtt) cc_final: 0.7004 (mtp) REVERT: D 714 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7670 (tt0) REVERT: D 796 PHE cc_start: 0.8874 (m-80) cc_final: 0.8016 (m-80) REVERT: D 807 MET cc_start: 0.8896 (mtp) cc_final: 0.8319 (tpp) outliers start: 20 outliers final: 3 residues processed: 678 average time/residue: 0.4092 time to fit residues: 430.6567 Evaluate side-chains 370 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 366 time to evaluate : 3.361 ------------------------------------------------------------------------------- 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: 6.9990 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: 8.9990 chunk 321 optimal weight: 10.0000 overall best weight: 2.2720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 587 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS B 219 HIS B 246 GLN 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 569 ASN ** 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 359 ASN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2640 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= 0.223 Angle : 0.601 8.475 38714 Z= 0.323 Chirality : 0.042 0.249 4304 Planarity : 0.005 0.080 4878 Dihedral : 6.492 85.335 3862 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % 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: -2.54 (0.12), residues: 3526 helix: -1.25 (0.11), residues: 1664 sheet: -1.68 (0.23), residues: 440 loop : -2.07 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 323 HIS 0.008 0.001 HIS B 93 PHE 0.023 0.002 PHE C 546 TYR 0.021 0.002 TYR B 77 ARG 0.015 0.001 ARG B 308 *********************** 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 484 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 483 time to evaluate : 2.993 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: A 362 GLU cc_start: 0.7928 (pp20) cc_final: 0.7685 (pp20) REVERT: A 419 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7727 (mp0) REVERT: A 514 VAL cc_start: 0.9157 (m) cc_final: 0.8891 (t) REVERT: A 669 LYS cc_start: 0.9196 (pttm) cc_final: 0.8735 (tptt) REVERT: A 811 LEU cc_start: 0.6801 (mp) cc_final: 0.6549 (tt) REVERT: A 880 MET cc_start: 0.3889 (tmm) cc_final: 0.3644 (tmm) REVERT: A 924 MET cc_start: 0.7001 (mmt) cc_final: 0.6340 (tpt) REVERT: A 1022 VAL cc_start: 0.8442 (t) cc_final: 0.8221 (t) REVERT: B 78 ASP cc_start: 0.8709 (t0) cc_final: 0.8297 (p0) REVERT: B 113 MET cc_start: 0.8363 (mmm) cc_final: 0.7839 (mmm) REVERT: B 232 LEU cc_start: 0.9138 (tp) cc_final: 0.8912 (tp) REVERT: B 380 MET cc_start: 0.5723 (pmm) cc_final: 0.5107 (pmm) REVERT: B 527 MET cc_start: 0.7942 (mtm) cc_final: 0.7695 (mmt) REVERT: B 541 PHE cc_start: 0.7294 (t80) cc_final: 0.6694 (t80) REVERT: B 585 MET cc_start: 0.9095 (mmm) cc_final: 0.7706 (mmt) REVERT: B 594 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7195 (ptm160) REVERT: B 657 GLU cc_start: 0.8680 (tp30) cc_final: 0.8375 (tp30) REVERT: B 715 ARG cc_start: 0.7768 (tpm170) cc_final: 0.7099 (mmp80) REVERT: B 721 MET cc_start: 0.7924 (ttp) cc_final: 0.7089 (tpt) REVERT: C 48 ASP cc_start: 0.8562 (t0) cc_final: 0.8356 (t0) REVERT: C 55 SER cc_start: 0.8964 (m) cc_final: 0.8754 (t) REVERT: C 189 GLU cc_start: 0.7515 (tp30) cc_final: 0.7230 (tp30) REVERT: C 407 MET cc_start: 0.7769 (mpp) cc_final: 0.7416 (mpp) REVERT: C 419 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7676 (mp0) REVERT: C 533 TYR cc_start: 0.8524 (t80) cc_final: 0.8136 (t80) REVERT: C 574 PHE cc_start: 0.7919 (t80) cc_final: 0.7595 (t80) REVERT: C 580 SER cc_start: 0.8447 (m) cc_final: 0.8083 (p) REVERT: C 581 LEU cc_start: 0.8934 (tp) cc_final: 0.8658 (tp) REVERT: C 623 PHE cc_start: 0.8818 (m-10) cc_final: 0.8485 (m-80) REVERT: C 669 LYS cc_start: 0.9047 (tptt) cc_final: 0.8659 (tptp) REVERT: C 798 ILE cc_start: 0.8814 (mt) cc_final: 0.8606 (tp) REVERT: D 330 GLU cc_start: 0.8453 (pt0) cc_final: 0.8082 (pm20) REVERT: D 527 MET cc_start: 0.8083 (mtm) cc_final: 0.7475 (mmt) REVERT: D 531 PHE cc_start: 0.8167 (m-10) cc_final: 0.7854 (m-10) REVERT: D 596 LEU cc_start: 0.8468 (mm) cc_final: 0.7857 (tp) REVERT: D 616 TYR cc_start: 0.9342 (t80) cc_final: 0.9048 (t80) REVERT: D 657 GLU cc_start: 0.8656 (tp30) cc_final: 0.8295 (tp30) REVERT: D 673 TYR cc_start: 0.8047 (t80) cc_final: 0.7731 (t80) REVERT: D 684 ARG cc_start: 0.7716 (mpt180) cc_final: 0.7296 (tpm170) REVERT: D 714 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7709 (tt0) REVERT: D 721 MET cc_start: 0.7953 (ttp) cc_final: 0.7655 (tpp) REVERT: D 748 LEU cc_start: 0.6634 (tt) cc_final: 0.6334 (pp) REVERT: D 807 MET cc_start: 0.8797 (mtp) cc_final: 0.8252 (tpp) outliers start: 1 outliers final: 0 residues processed: 484 average time/residue: 0.3915 time to fit residues: 302.0493 Evaluate side-chains 337 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 3.123 ------------------------------------------------------------------------------- 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: 0.0770 chunk 99 optimal weight: 10.0000 chunk 267 optimal weight: 20.0000 chunk 218 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 322 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 319 optimal weight: 0.0770 chunk 109 optimal weight: 8.9990 chunk 258 optimal weight: 30.0000 overall best weight: 3.0302 ------------------------------------------------------------------------------- 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 350 ASN A 412 HIS ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** C 950 HIS ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 435 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28652 Z= 0.262 Angle : 0.597 9.235 38714 Z= 0.316 Chirality : 0.043 0.251 4304 Planarity : 0.005 0.079 4878 Dihedral : 6.216 80.373 3862 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.16 % Allowed : 2.70 % 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: -1.63 (0.13), residues: 3526 helix: -0.25 (0.12), residues: 1678 sheet: -1.80 (0.24), residues: 410 loop : -1.77 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 323 HIS 0.007 0.002 HIS B 93 PHE 0.020 0.002 PHE C 546 TYR 0.026 0.002 TYR A 732 ARG 0.005 0.001 ARG C 715 *********************** 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 426 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 421 time to evaluate : 3.083 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: A 362 GLU cc_start: 0.7932 (pp20) cc_final: 0.7685 (pp20) REVERT: A 407 MET cc_start: 0.7852 (mpp) cc_final: 0.7647 (mpp) REVERT: A 419 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7813 (mp0) REVERT: A 514 VAL cc_start: 0.9234 (m) cc_final: 0.9032 (t) REVERT: A 669 LYS cc_start: 0.9156 (pttm) cc_final: 0.8764 (tptt) REVERT: A 899 ARG cc_start: 0.1810 (mtm-85) cc_final: 0.1587 (ttp-110) REVERT: A 924 MET cc_start: 0.7165 (mmt) cc_final: 0.6587 (mmm) REVERT: B 78 ASP cc_start: 0.8725 (t0) cc_final: 0.8380 (p0) REVERT: B 232 LEU cc_start: 0.9268 (tp) cc_final: 0.8969 (tp) REVERT: B 380 MET cc_start: 0.6117 (pmm) cc_final: 0.5665 (pmm) REVERT: B 405 TYR cc_start: 0.7652 (m-10) cc_final: 0.7422 (m-10) REVERT: B 527 MET cc_start: 0.8067 (mtm) cc_final: 0.7820 (mmt) REVERT: B 585 MET cc_start: 0.9206 (mmm) cc_final: 0.7656 (mmt) REVERT: B 594 ARG cc_start: 0.8089 (mtp-110) cc_final: 0.7266 (ptm160) REVERT: B 657 GLU cc_start: 0.8728 (tp30) cc_final: 0.8350 (pt0) REVERT: B 715 ARG cc_start: 0.7814 (tpm170) cc_final: 0.7101 (mmp80) REVERT: B 721 MET cc_start: 0.8055 (ttp) cc_final: 0.7261 (tpt) REVERT: B 763 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7667 (tptt) REVERT: C 48 ASP cc_start: 0.8594 (t0) cc_final: 0.8387 (t0) REVERT: C 189 GLU cc_start: 0.7500 (tp30) cc_final: 0.7261 (tp30) REVERT: C 407 MET cc_start: 0.7990 (mpp) cc_final: 0.7492 (mpp) REVERT: C 541 PHE cc_start: 0.8396 (t80) cc_final: 0.8137 (t80) REVERT: C 574 PHE cc_start: 0.7908 (t80) cc_final: 0.7645 (t80) REVERT: C 669 LYS cc_start: 0.9071 (tptt) cc_final: 0.8750 (tptp) REVERT: C 819 ARG cc_start: 0.7000 (mmp80) cc_final: 0.5728 (ttp80) REVERT: D 527 MET cc_start: 0.8077 (mtm) cc_final: 0.7559 (mmt) REVERT: D 531 PHE cc_start: 0.8201 (m-10) cc_final: 0.7870 (m-10) REVERT: D 596 LEU cc_start: 0.8667 (mm) cc_final: 0.8116 (tp) REVERT: D 616 TYR cc_start: 0.9445 (t80) cc_final: 0.9166 (t80) REVERT: D 657 GLU cc_start: 0.8645 (tp30) cc_final: 0.8326 (tp30) REVERT: D 673 TYR cc_start: 0.8061 (t80) cc_final: 0.7696 (t80) REVERT: D 714 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7521 (tt0) REVERT: D 715 ARG cc_start: 0.7795 (tmt-80) cc_final: 0.7359 (mmm160) REVERT: D 721 MET cc_start: 0.7954 (ttp) cc_final: 0.7535 (tpt) REVERT: D 748 LEU cc_start: 0.6593 (tt) cc_final: 0.6233 (pp) REVERT: D 807 MET cc_start: 0.8779 (mtp) cc_final: 0.8215 (tpp) outliers start: 5 outliers final: 2 residues processed: 426 average time/residue: 0.3779 time to fit residues: 260.2537 Evaluate side-chains 318 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 316 time to evaluate : 3.251 ------------------------------------------------------------------------------- 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: 6.9990 chunk 242 optimal weight: 0.0050 chunk 167 optimal weight: 8.9990 chunk 35 optimal weight: 0.0020 chunk 153 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 chunk 342 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 306 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 overall best weight: 4.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** 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 112 GLN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 HIS D 435 HIS D 619 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28652 Z= 0.324 Angle : 0.643 9.158 38714 Z= 0.338 Chirality : 0.044 0.199 4304 Planarity : 0.005 0.074 4878 Dihedral : 6.258 82.523 3862 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.16 % Allowed : 3.56 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.03 % 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: -1.40 (0.14), residues: 3526 helix: -0.00 (0.13), residues: 1690 sheet: -1.83 (0.26), residues: 388 loop : -1.72 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 323 HIS 0.007 0.002 HIS B 93 PHE 0.023 0.002 PHE B 88 TYR 0.029 0.002 TYR A 732 ARG 0.007 0.001 ARG C 594 *********************** 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 389 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 384 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8988 (mp0) cc_final: 0.8438 (mp0) REVERT: A 419 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7953 (mp0) REVERT: A 669 LYS cc_start: 0.9146 (pttm) cc_final: 0.8664 (tptt) REVERT: A 899 ARG cc_start: 0.2262 (mtm-85) cc_final: 0.1704 (ttp-110) REVERT: A 924 MET cc_start: 0.7302 (mmt) cc_final: 0.6836 (tpt) REVERT: A 996 GLU cc_start: 0.6953 (tt0) cc_final: 0.6600 (mp0) REVERT: B 78 ASP cc_start: 0.8720 (t0) cc_final: 0.8412 (p0) REVERT: B 113 MET cc_start: 0.8294 (mmm) cc_final: 0.7956 (mmm) REVERT: B 225 LEU cc_start: 0.9090 (mt) cc_final: 0.8663 (mp) REVERT: B 309 ARG cc_start: 0.7329 (mmp80) cc_final: 0.7051 (mmp80) REVERT: B 527 MET cc_start: 0.8255 (mtm) cc_final: 0.7907 (mmt) REVERT: B 594 ARG cc_start: 0.8050 (mtp-110) cc_final: 0.7588 (ptm160) REVERT: B 657 GLU cc_start: 0.8611 (tp30) cc_final: 0.8314 (tp30) REVERT: B 715 ARG cc_start: 0.7906 (tpm170) cc_final: 0.7133 (mmp80) REVERT: B 721 MET cc_start: 0.7954 (ttp) cc_final: 0.7650 (ttp) REVERT: C 189 GLU cc_start: 0.7380 (tp30) cc_final: 0.7155 (tp30) REVERT: C 407 MET cc_start: 0.7950 (mpp) cc_final: 0.7448 (mpp) REVERT: C 524 GLU cc_start: 0.8338 (pm20) cc_final: 0.8061 (pm20) REVERT: C 574 PHE cc_start: 0.7943 (t80) cc_final: 0.7686 (t80) REVERT: C 669 LYS cc_start: 0.9090 (tptt) cc_final: 0.8640 (tptp) REVERT: C 819 ARG cc_start: 0.6817 (mmp80) cc_final: 0.5588 (ttp80) REVERT: C 883 HIS cc_start: 0.5732 (p90) cc_final: 0.5317 (p90) REVERT: D 330 GLU cc_start: 0.8506 (pt0) cc_final: 0.8245 (pt0) REVERT: D 527 MET cc_start: 0.8103 (mtm) cc_final: 0.7199 (mmp) REVERT: D 531 PHE cc_start: 0.8244 (m-10) cc_final: 0.7970 (m-10) REVERT: D 596 LEU cc_start: 0.8618 (mm) cc_final: 0.8081 (tp) REVERT: D 616 TYR cc_start: 0.9475 (t80) cc_final: 0.9205 (t80) REVERT: D 657 GLU cc_start: 0.8724 (tp30) cc_final: 0.8421 (tp30) REVERT: D 721 MET cc_start: 0.7910 (ttp) cc_final: 0.7527 (tpt) REVERT: D 748 LEU cc_start: 0.6840 (tt) cc_final: 0.6495 (pp) REVERT: D 799 LEU cc_start: 0.8930 (tp) cc_final: 0.8701 (tp) REVERT: D 807 MET cc_start: 0.8791 (mtp) cc_final: 0.8221 (tpp) REVERT: D 809 VAL cc_start: 0.8788 (t) cc_final: 0.8158 (t) outliers start: 5 outliers final: 3 residues processed: 389 average time/residue: 0.3703 time to fit residues: 234.7300 Evaluate side-chains 299 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 296 time to evaluate : 3.379 ------------------------------------------------------------------------------- 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: 7.9990 chunk 194 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 254 optimal weight: 0.0770 chunk 141 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 236 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.0050 chunk 307 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 overall best weight: 0.7954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 412 HIS A 586 GLN ** A 619 ASN ** 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 726 ASN D 435 HIS ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28652 Z= 0.147 Angle : 0.531 10.158 38714 Z= 0.275 Chirality : 0.042 0.301 4304 Planarity : 0.004 0.068 4878 Dihedral : 5.694 83.758 3862 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.63 % 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: -0.97 (0.14), residues: 3526 helix: 0.46 (0.13), residues: 1692 sheet: -1.71 (0.26), residues: 386 loop : -1.61 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 323 HIS 0.006 0.001 HIS B 93 PHE 0.018 0.001 PHE C 546 TYR 0.024 0.001 TYR A 732 ARG 0.005 0.000 ARG B 178 *********************** 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 408 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 407 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: A 25 GLU cc_start: 0.8844 (mp0) cc_final: 0.8318 (mp0) REVERT: A 419 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7985 (mp0) REVERT: A 540 LEU cc_start: 0.9089 (tp) cc_final: 0.8846 (tp) REVERT: A 669 LYS cc_start: 0.9204 (pttm) cc_final: 0.8760 (tptt) REVERT: A 899 ARG cc_start: 0.2310 (mtm-85) cc_final: 0.1614 (ttp-110) REVERT: A 924 MET cc_start: 0.7315 (mmt) cc_final: 0.6841 (tpt) REVERT: B 78 ASP cc_start: 0.8683 (t0) cc_final: 0.8375 (p0) REVERT: B 113 MET cc_start: 0.8344 (mmm) cc_final: 0.7970 (mmm) REVERT: B 225 LEU cc_start: 0.8951 (mt) cc_final: 0.8401 (mp) REVERT: B 247 ILE cc_start: 0.9210 (pt) cc_final: 0.9003 (pt) REVERT: B 309 ARG cc_start: 0.7241 (mmp80) cc_final: 0.6485 (mmm160) REVERT: B 527 MET cc_start: 0.8151 (mtm) cc_final: 0.7831 (mmt) REVERT: B 585 MET cc_start: 0.9184 (mmm) cc_final: 0.8091 (mmm) REVERT: B 594 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7147 (ptt90) REVERT: B 657 GLU cc_start: 0.8625 (tp30) cc_final: 0.8125 (pt0) REVERT: B 715 ARG cc_start: 0.7853 (tpm170) cc_final: 0.7182 (mmp80) REVERT: B 721 MET cc_start: 0.7990 (ttp) cc_final: 0.7732 (ttp) REVERT: C 123 SER cc_start: 0.8807 (m) cc_final: 0.8543 (p) REVERT: C 284 LEU cc_start: 0.9631 (mt) cc_final: 0.9344 (mt) REVERT: C 574 PHE cc_start: 0.7855 (t80) cc_final: 0.7597 (t80) REVERT: C 669 LYS cc_start: 0.9035 (tptt) cc_final: 0.8668 (tptp) REVERT: C 819 ARG cc_start: 0.6873 (mmp80) cc_final: 0.5634 (ttp80) REVERT: C 883 HIS cc_start: 0.5728 (p90) cc_final: 0.5326 (p90) REVERT: D 225 LEU cc_start: 0.8965 (mt) cc_final: 0.8408 (mp) REVERT: D 354 ILE cc_start: 0.8909 (pt) cc_final: 0.8671 (tp) REVERT: D 527 MET cc_start: 0.7973 (mtm) cc_final: 0.7015 (mmp) REVERT: D 531 PHE cc_start: 0.8025 (m-10) cc_final: 0.7778 (m-10) REVERT: D 596 LEU cc_start: 0.8584 (mm) cc_final: 0.8084 (tp) REVERT: D 616 TYR cc_start: 0.9484 (t80) cc_final: 0.9242 (t80) REVERT: D 657 GLU cc_start: 0.8747 (tp30) cc_final: 0.8423 (tp30) REVERT: D 715 ARG cc_start: 0.7753 (tmt-80) cc_final: 0.7502 (mmm160) REVERT: D 721 MET cc_start: 0.7926 (ttp) cc_final: 0.7529 (tpt) REVERT: D 748 LEU cc_start: 0.6975 (tt) cc_final: 0.6764 (pp) REVERT: D 799 LEU cc_start: 0.9004 (tp) cc_final: 0.8782 (tp) REVERT: D 807 MET cc_start: 0.8780 (mtp) cc_final: 0.8164 (tpp) REVERT: D 812 ILE cc_start: 0.7483 (tp) cc_final: 0.7276 (mm) outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.3741 time to fit residues: 247.9348 Evaluate side-chains 300 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 3.200 ------------------------------------------------------------------------------- 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: 2.9990 chunk 308 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 342 optimal weight: 0.0470 chunk 284 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN B 10 ASN B 355 ASN B 586 GLN ** 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7810 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28652 Z= 0.171 Angle : 0.534 9.153 38714 Z= 0.277 Chirality : 0.041 0.191 4304 Planarity : 0.004 0.067 4878 Dihedral : 5.584 83.863 3862 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % 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: -0.83 (0.14), residues: 3526 helix: 0.59 (0.13), residues: 1696 sheet: -1.71 (0.25), residues: 412 loop : -1.55 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 323 HIS 0.004 0.001 HIS B 93 PHE 0.016 0.001 PHE A 546 TYR 0.021 0.001 TYR A 732 ARG 0.004 0.000 ARG D 178 *********************** 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 374 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8842 (mp0) cc_final: 0.8297 (mp0) REVERT: A 65 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8515 (mm-40) REVERT: A 540 LEU cc_start: 0.9092 (tp) cc_final: 0.8869 (tp) REVERT: A 669 LYS cc_start: 0.9161 (pttm) cc_final: 0.8765 (tptt) REVERT: A 924 MET cc_start: 0.7316 (mmt) cc_final: 0.6817 (tpt) REVERT: B 78 ASP cc_start: 0.8690 (t0) cc_final: 0.8419 (p0) REVERT: B 225 LEU cc_start: 0.8970 (mt) cc_final: 0.8568 (mt) REVERT: B 247 ILE cc_start: 0.9206 (pt) cc_final: 0.8886 (pt) REVERT: B 309 ARG cc_start: 0.7386 (mmp80) cc_final: 0.6390 (mmm160) REVERT: B 527 MET cc_start: 0.8223 (mtm) cc_final: 0.7495 (mmt) REVERT: B 531 PHE cc_start: 0.7731 (m-10) cc_final: 0.7501 (m-10) REVERT: B 585 MET cc_start: 0.9220 (mmm) cc_final: 0.8880 (mmm) REVERT: B 594 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7168 (ptt90) REVERT: B 657 GLU cc_start: 0.8661 (tp30) cc_final: 0.8141 (pt0) REVERT: B 721 MET cc_start: 0.7933 (ttp) cc_final: 0.7697 (ttp) REVERT: B 817 LYS cc_start: 0.7246 (tptt) cc_final: 0.6776 (ptmm) REVERT: C 123 SER cc_start: 0.8769 (m) cc_final: 0.8567 (p) REVERT: C 362 GLU cc_start: 0.7859 (pp20) cc_final: 0.7569 (pp20) REVERT: C 407 MET cc_start: 0.8193 (mpp) cc_final: 0.7836 (mpp) REVERT: C 498 LEU cc_start: 0.9050 (pp) cc_final: 0.8789 (pp) REVERT: C 524 GLU cc_start: 0.8265 (pm20) cc_final: 0.8026 (pm20) REVERT: C 540 LEU cc_start: 0.9017 (tp) cc_final: 0.8811 (tp) REVERT: C 819 ARG cc_start: 0.6841 (mmp80) cc_final: 0.5587 (ttp80) REVERT: C 883 HIS cc_start: 0.5799 (p90) cc_final: 0.5366 (p90) REVERT: D 225 LEU cc_start: 0.8956 (mt) cc_final: 0.8423 (mp) REVERT: D 235 ILE cc_start: 0.9489 (pt) cc_final: 0.9274 (pt) REVERT: D 527 MET cc_start: 0.8028 (mtm) cc_final: 0.7037 (mmp) REVERT: D 531 PHE cc_start: 0.8010 (m-10) cc_final: 0.7764 (m-10) REVERT: D 596 LEU cc_start: 0.8543 (mm) cc_final: 0.8041 (tp) REVERT: D 616 TYR cc_start: 0.9497 (t80) cc_final: 0.9277 (t80) REVERT: D 657 GLU cc_start: 0.8749 (tp30) cc_final: 0.8436 (tp30) REVERT: D 715 ARG cc_start: 0.7765 (tmt-80) cc_final: 0.7476 (mmp80) REVERT: D 721 MET cc_start: 0.7876 (ttp) cc_final: 0.7566 (tpt) REVERT: D 748 LEU cc_start: 0.7078 (tt) cc_final: 0.6857 (pp) REVERT: D 799 LEU cc_start: 0.9008 (tp) cc_final: 0.8805 (tp) REVERT: D 807 MET cc_start: 0.8709 (mtp) cc_final: 0.8472 (mtt) REVERT: D 812 ILE cc_start: 0.7649 (tp) cc_final: 0.7403 (mm) outliers start: 1 outliers final: 0 residues processed: 374 average time/residue: 0.3728 time to fit residues: 228.6550 Evaluate side-chains 295 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 3.171 ------------------------------------------------------------------------------- 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: 9.9990 chunk 38 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 341 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 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 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 569 ASN ** A 619 ASN ** 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 ** 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28652 Z= 0.336 Angle : 0.647 10.291 38714 Z= 0.336 Chirality : 0.044 0.179 4304 Planarity : 0.005 0.069 4878 Dihedral : 5.940 88.936 3862 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: -1.01 (0.14), residues: 3526 helix: 0.46 (0.13), residues: 1682 sheet: -1.81 (0.25), residues: 410 loop : -1.63 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 766 HIS 0.005 0.002 HIS B 219 PHE 0.041 0.002 PHE C1028 TYR 0.027 0.002 TYR C 732 ARG 0.008 0.001 ARG D 300 *********************** 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 351 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8906 (mp0) cc_final: 0.8378 (mp0) REVERT: A 540 LEU cc_start: 0.9075 (tp) cc_final: 0.8858 (tp) REVERT: A 669 LYS cc_start: 0.9125 (pttm) cc_final: 0.8827 (tptt) REVERT: A 924 MET cc_start: 0.7387 (mmt) cc_final: 0.6913 (tpt) REVERT: B 225 LEU cc_start: 0.9008 (mt) cc_final: 0.8630 (mp) REVERT: B 309 ARG cc_start: 0.7515 (mmp80) cc_final: 0.6530 (mmm160) REVERT: B 527 MET cc_start: 0.8342 (mtm) cc_final: 0.7926 (mmt) REVERT: B 594 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7261 (ptm-80) REVERT: B 657 GLU cc_start: 0.8651 (tp30) cc_final: 0.8349 (tp30) REVERT: B 721 MET cc_start: 0.7998 (ttp) cc_final: 0.7772 (ttp) REVERT: B 799 LEU cc_start: 0.8966 (tp) cc_final: 0.8653 (tp) REVERT: B 817 LYS cc_start: 0.7172 (tptt) cc_final: 0.6791 (ptmm) REVERT: C 407 MET cc_start: 0.8104 (mpp) cc_final: 0.7719 (mpp) REVERT: C 574 PHE cc_start: 0.7846 (t80) cc_final: 0.7568 (t80) REVERT: C 607 PHE cc_start: 0.9203 (t80) cc_final: 0.8997 (t80) REVERT: C 819 ARG cc_start: 0.6686 (mmp80) cc_final: 0.5535 (ttp80) REVERT: D 225 LEU cc_start: 0.9013 (mt) cc_final: 0.8581 (mp) REVERT: D 503 MET cc_start: 0.6009 (mmt) cc_final: 0.5797 (mmm) REVERT: D 527 MET cc_start: 0.8133 (mtm) cc_final: 0.7193 (mmp) REVERT: D 531 PHE cc_start: 0.8136 (m-10) cc_final: 0.7889 (m-10) REVERT: D 596 LEU cc_start: 0.8474 (mm) cc_final: 0.7968 (tp) REVERT: D 597 SER cc_start: 0.9096 (p) cc_final: 0.8843 (m) REVERT: D 657 GLU cc_start: 0.8762 (tp30) cc_final: 0.8547 (tp30) REVERT: D 721 MET cc_start: 0.7828 (ttp) cc_final: 0.7499 (tpt) REVERT: D 799 LEU cc_start: 0.9016 (tp) cc_final: 0.8700 (tp) REVERT: D 807 MET cc_start: 0.8729 (mtp) cc_final: 0.8502 (mtt) REVERT: D 812 ILE cc_start: 0.7712 (tp) cc_final: 0.7481 (mm) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.3758 time to fit residues: 216.3764 Evaluate side-chains 266 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.985 ------------------------------------------------------------------------------- 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: 0.2980 chunk 136 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** 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 359 ASN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 435 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28652 Z= 0.187 Angle : 0.566 11.833 38714 Z= 0.290 Chirality : 0.042 0.169 4304 Planarity : 0.004 0.066 4878 Dihedral : 5.643 87.568 3862 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -0.82 (0.14), residues: 3526 helix: 0.66 (0.13), residues: 1678 sheet: -1.77 (0.25), residues: 392 loop : -1.58 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 323 HIS 0.004 0.001 HIS B 93 PHE 0.027 0.001 PHE C1028 TYR 0.015 0.001 TYR B 673 ARG 0.004 0.000 ARG D 300 *********************** 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 348 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8788 (mp0) cc_final: 0.8325 (mp0) REVERT: A 527 MET cc_start: 0.7474 (mmt) cc_final: 0.7010 (mmm) REVERT: A 540 LEU cc_start: 0.9097 (tp) cc_final: 0.8884 (tp) REVERT: A 669 LYS cc_start: 0.9128 (pttm) cc_final: 0.8807 (tptt) REVERT: A 924 MET cc_start: 0.7376 (mmt) cc_final: 0.6897 (tpt) REVERT: B 225 LEU cc_start: 0.8910 (mt) cc_final: 0.8469 (mp) REVERT: B 309 ARG cc_start: 0.7513 (mmp80) cc_final: 0.6542 (mmm160) REVERT: B 527 MET cc_start: 0.8286 (mtm) cc_final: 0.7579 (mmt) REVERT: B 531 PHE cc_start: 0.7813 (m-10) cc_final: 0.7559 (m-10) REVERT: B 585 MET cc_start: 0.9155 (mmm) cc_final: 0.8340 (mmm) REVERT: B 594 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7287 (ptm-80) REVERT: B 657 GLU cc_start: 0.8626 (tp30) cc_final: 0.8109 (pt0) REVERT: B 721 MET cc_start: 0.7940 (ttp) cc_final: 0.7708 (ttp) REVERT: B 817 LYS cc_start: 0.7227 (tptt) cc_final: 0.6862 (ptmm) REVERT: C 407 MET cc_start: 0.8376 (mpp) cc_final: 0.8109 (mpp) REVERT: C 574 PHE cc_start: 0.7876 (t80) cc_final: 0.7584 (t80) REVERT: C 819 ARG cc_start: 0.6629 (mmp80) cc_final: 0.5513 (ttp80) REVERT: D 225 LEU cc_start: 0.8951 (mt) cc_final: 0.8515 (mp) REVERT: D 503 MET cc_start: 0.5707 (mmt) cc_final: 0.5470 (mmm) REVERT: D 527 MET cc_start: 0.8053 (mtm) cc_final: 0.7045 (mmp) REVERT: D 531 PHE cc_start: 0.8063 (m-10) cc_final: 0.7817 (m-10) REVERT: D 596 LEU cc_start: 0.8525 (mm) cc_final: 0.8089 (tp) REVERT: D 597 SER cc_start: 0.9089 (p) cc_final: 0.8778 (m) REVERT: D 657 GLU cc_start: 0.8735 (tp30) cc_final: 0.8473 (tp30) REVERT: D 721 MET cc_start: 0.7843 (ttp) cc_final: 0.7532 (tpt) REVERT: D 812 ILE cc_start: 0.7807 (tp) cc_final: 0.7581 (mm) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.3585 time to fit residues: 206.7802 Evaluate side-chains 276 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.954 ------------------------------------------------------------------------------- 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: 4.9990 chunk 326 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 chunk 317 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 287 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 chunk 316 optimal weight: 0.9980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 GLN ** 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 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5081 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= 0.217 Angle : 0.579 11.954 38714 Z= 0.299 Chirality : 0.042 0.162 4304 Planarity : 0.004 0.067 4878 Dihedral : 5.598 82.742 3862 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -0.82 (0.14), residues: 3526 helix: 0.67 (0.13), residues: 1682 sheet: -1.76 (0.25), residues: 394 loop : -1.61 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 323 HIS 0.004 0.001 HIS D 93 PHE 0.018 0.001 PHE C1028 TYR 0.022 0.001 TYR D 768 ARG 0.004 0.000 ARG D 300 *********************** 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 338 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8795 (mp0) cc_final: 0.8306 (mp0) REVERT: A 527 MET cc_start: 0.7427 (mmt) cc_final: 0.6935 (mmm) REVERT: A 540 LEU cc_start: 0.9108 (tp) cc_final: 0.8896 (tp) REVERT: A 546 PHE cc_start: 0.7917 (t80) cc_final: 0.7575 (t80) REVERT: A 669 LYS cc_start: 0.9114 (pttm) cc_final: 0.8809 (tptt) REVERT: A 721 MET cc_start: 0.8391 (ppp) cc_final: 0.8163 (ppp) REVERT: A 924 MET cc_start: 0.7499 (mmt) cc_final: 0.7008 (tpt) REVERT: B 225 LEU cc_start: 0.8925 (mt) cc_final: 0.8511 (mp) REVERT: B 309 ARG cc_start: 0.7506 (mmp80) cc_final: 0.6720 (mmm160) REVERT: B 527 MET cc_start: 0.8266 (mtm) cc_final: 0.7591 (mmt) REVERT: B 531 PHE cc_start: 0.7838 (m-10) cc_final: 0.7578 (m-10) REVERT: B 585 MET cc_start: 0.9169 (mmm) cc_final: 0.8382 (mmm) REVERT: B 594 ARG cc_start: 0.7848 (mtp-110) cc_final: 0.7432 (ptm-80) REVERT: B 657 GLU cc_start: 0.8630 (tp30) cc_final: 0.8108 (pt0) REVERT: B 721 MET cc_start: 0.7925 (ttp) cc_final: 0.7709 (ttp) REVERT: B 817 LYS cc_start: 0.7275 (tptt) cc_final: 0.6909 (ptmm) REVERT: C 407 MET cc_start: 0.8212 (mpp) cc_final: 0.7947 (mpp) REVERT: C 463 MET cc_start: 0.8419 (tpp) cc_final: 0.8038 (tpt) REVERT: C 540 LEU cc_start: 0.8925 (tp) cc_final: 0.8724 (tp) REVERT: C 574 PHE cc_start: 0.7784 (t80) cc_final: 0.7461 (t80) REVERT: C 819 ARG cc_start: 0.6555 (mmp80) cc_final: 0.5552 (ttt-90) REVERT: D 225 LEU cc_start: 0.8939 (mt) cc_final: 0.8506 (mp) REVERT: D 503 MET cc_start: 0.5620 (mmt) cc_final: 0.5344 (mmm) REVERT: D 527 MET cc_start: 0.8078 (mtm) cc_final: 0.7114 (mmp) REVERT: D 531 PHE cc_start: 0.8072 (m-10) cc_final: 0.7823 (m-10) REVERT: D 596 LEU cc_start: 0.8510 (mm) cc_final: 0.8078 (tp) REVERT: D 597 SER cc_start: 0.9082 (p) cc_final: 0.8831 (m) REVERT: D 657 GLU cc_start: 0.8784 (tp30) cc_final: 0.8516 (tp30) REVERT: D 708 MET cc_start: 0.7931 (ptt) cc_final: 0.7668 (ptt) REVERT: D 721 MET cc_start: 0.7803 (ttp) cc_final: 0.7487 (tpt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.3561 time to fit residues: 199.0886 Evaluate side-chains 275 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 3.389 ------------------------------------------------------------------------------- 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: 3.9990 chunk 336 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 233 optimal weight: 0.0670 chunk 352 optimal weight: 0.8980 chunk 324 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 GLN ** 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 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28652 Z= 0.191 Angle : 0.563 11.756 38714 Z= 0.289 Chirality : 0.042 0.170 4304 Planarity : 0.004 0.066 4878 Dihedral : 5.477 83.055 3862 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.76 (0.14), residues: 3526 helix: 0.73 (0.13), residues: 1682 sheet: -1.72 (0.25), residues: 394 loop : -1.59 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 323 HIS 0.003 0.001 HIS D 93 PHE 0.015 0.001 PHE C1028 TYR 0.017 0.001 TYR D 768 ARG 0.003 0.000 ARG D 300 ********************** 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 341 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8779 (mp0) cc_final: 0.8287 (mp0) REVERT: A 463 MET cc_start: 0.8449 (tpp) cc_final: 0.8098 (tpt) REVERT: A 527 MET cc_start: 0.7352 (mmt) cc_final: 0.6921 (mmm) REVERT: A 540 LEU cc_start: 0.9088 (tp) cc_final: 0.8874 (tp) REVERT: A 669 LYS cc_start: 0.9147 (pttm) cc_final: 0.8836 (tptt) REVERT: A 924 MET cc_start: 0.7578 (mmt) cc_final: 0.7053 (tpt) REVERT: B 225 LEU cc_start: 0.8926 (mt) cc_final: 0.8354 (mp) REVERT: B 309 ARG cc_start: 0.7495 (mmp80) cc_final: 0.6690 (mmm160) REVERT: B 450 TYR cc_start: 0.4971 (m-80) cc_final: 0.4016 (m-10) REVERT: B 463 MET cc_start: 0.4986 (mmp) cc_final: 0.4397 (mmp) REVERT: B 527 MET cc_start: 0.8245 (mtm) cc_final: 0.7560 (mmt) REVERT: B 531 PHE cc_start: 0.7865 (m-10) cc_final: 0.7601 (m-10) REVERT: B 585 MET cc_start: 0.9138 (mmm) cc_final: 0.8372 (mmm) REVERT: B 594 ARG cc_start: 0.7831 (mtp-110) cc_final: 0.7499 (ptm-80) REVERT: B 657 GLU cc_start: 0.8624 (tp30) cc_final: 0.8100 (pt0) REVERT: B 721 MET cc_start: 0.7878 (ttp) cc_final: 0.7666 (ttp) REVERT: B 813 GLU cc_start: 0.7041 (tp30) cc_final: 0.6646 (mt-10) REVERT: B 817 LYS cc_start: 0.7308 (tptt) cc_final: 0.7081 (ptmm) REVERT: C 407 MET cc_start: 0.8214 (mpp) cc_final: 0.7976 (mpp) REVERT: C 463 MET cc_start: 0.8446 (tpp) cc_final: 0.7946 (tpt) REVERT: C 574 PHE cc_start: 0.7896 (t80) cc_final: 0.7529 (t80) REVERT: C 819 ARG cc_start: 0.6227 (mmp80) cc_final: 0.5310 (ttt-90) REVERT: D 225 LEU cc_start: 0.8922 (mt) cc_final: 0.8522 (mp) REVERT: D 503 MET cc_start: 0.5586 (mmt) cc_final: 0.5299 (mmm) REVERT: D 527 MET cc_start: 0.8060 (mtm) cc_final: 0.7099 (mmp) REVERT: D 531 PHE cc_start: 0.8052 (m-10) cc_final: 0.7833 (m-10) REVERT: D 585 MET cc_start: 0.9096 (mmm) cc_final: 0.8042 (mmm) REVERT: D 596 LEU cc_start: 0.8480 (mm) cc_final: 0.8067 (tp) REVERT: D 597 SER cc_start: 0.9053 (p) cc_final: 0.8806 (m) REVERT: D 633 ILE cc_start: 0.8571 (pt) cc_final: 0.8297 (mm) REVERT: D 657 GLU cc_start: 0.8791 (tp30) cc_final: 0.8509 (tp30) REVERT: D 708 MET cc_start: 0.7922 (ptt) cc_final: 0.7650 (ptt) REVERT: D 721 MET cc_start: 0.7763 (ttp) cc_final: 0.7433 (tpt) REVERT: D 796 PHE cc_start: 0.8492 (m-80) cc_final: 0.8237 (m-80) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.3537 time to fit residues: 200.0040 Evaluate side-chains 274 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 3.438 ------------------------------------------------------------------------------- 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: 0.0060 chunk 299 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 258 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 281 optimal weight: 8.9990 chunk 117 optimal weight: 0.5980 chunk 288 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 GLN ** 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 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.100429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074298 restraints weight = 98811.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073512 restraints weight = 62966.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074327 restraints weight = 43904.815| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28652 Z= 0.166 Angle : 0.547 11.708 38714 Z= 0.280 Chirality : 0.041 0.161 4304 Planarity : 0.004 0.066 4878 Dihedral : 5.346 83.810 3862 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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 : 3.00 % 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: -0.67 (0.14), residues: 3526 helix: 0.81 (0.13), residues: 1682 sheet: -1.66 (0.25), residues: 394 loop : -1.56 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 323 HIS 0.003 0.001 HIS B 93 PHE 0.013 0.001 PHE C 546 TYR 0.019 0.001 TYR D 768 ARG 0.007 0.000 ARG A 545 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5568.10 seconds wall clock time: 102 minutes 55.25 seconds (6175.25 seconds total)