Starting phenix.real_space_refine on Tue Sep 24 06:09:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1l_40971/09_2024/8t1l_40971.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1l_40971/09_2024/8t1l_40971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1l_40971/09_2024/8t1l_40971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1l_40971/09_2024/8t1l_40971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1l_40971/09_2024/8t1l_40971.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1l_40971/09_2024/8t1l_40971.cif" } resolution = 4.83 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= 0.014 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 156 5.16 5 C 31198 2.51 5 N 9116 2.21 5 O 8990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49460 Number of models: 1 Model: "" Number of chains: 26 Chain: "E" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 888 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 693 Unresolved non-hydrogen dihedrals: 439 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 291 Chain: "A" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 2339 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 425} Link IDs: {'PTRANS': 33, 'TRANS': 438} Chain breaks: 4 Unresolved chain link angles: 33 Unresolved non-hydrogen bonds: 1457 Unresolved non-hydrogen angles: 1856 Unresolved non-hydrogen dihedrals: 1225 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 21, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 3, 'HIS:plan': 16, 'PHE:plan': 18, 'GLU:plan': 22, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 696 Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 784 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 495 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 267 Chain: "C" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 963 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 514 Unresolved non-hydrogen angles: 668 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 303 Chain: "D" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 801 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 10, 'TRANS': 150} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 721 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 315 Chain: "F" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 363 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 129 Chain: "G" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 605 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 515 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 223 Chain: "H" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 582 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 1, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 136 Chain: "I" Number of atoms: 6892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 6892 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 614} Link IDs: {'CIS': 1, 'PTRANS': 69, 'TRANS': 1040} Chain breaks: 17 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 2014 Unresolved non-hydrogen angles: 2543 Unresolved non-hydrogen dihedrals: 1588 Unresolved non-hydrogen chiralities: 236 Planarities with less than four sites: {'GLN:plan1': 40, 'HIS:plan': 8, 'TYR:plan': 6, 'ASN:plan1': 34, 'TRP:plan': 2, 'ASP:plan': 39, 'PHE:plan': 20, 'GLU:plan': 44, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 960 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1171 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 17, 'TRANS': 149} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 85 Chain: "K" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5051 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 222} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 694} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 790 Unresolved non-hydrogen dihedrals: 514 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 22, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 25, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 310 Chain: "L" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 3424 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 315} Link IDs: {'PTRANS': 25, 'TRANS': 533} Chain breaks: 6 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1022 Unresolved non-hydrogen angles: 1271 Unresolved non-hydrogen dihedrals: 814 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 36, 'HIS:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 528 Chain: "M" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1140 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'ASN:plan1': 6, 'HIS:plan': 2, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "O" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1013 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 10, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 169 Chain: "P" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 568 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 177 Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 754 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 173 Chain: "R" Number of atoms: 9771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1299, 9771 Classifications: {'peptide': 1299} Incomplete info: {'truncation_to_alanine': 220} Link IDs: {'CIS': 4, 'PTRANS': 69, 'TRANS': 1225} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 744 Unresolved non-hydrogen angles: 933 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 25, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 388 Chain: "S" Number of atoms: 5934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 5934 Classifications: {'peptide': 913} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PTRANS': 37, 'TRANS': 875} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1245 Unresolved non-hydrogen angles: 1551 Unresolved non-hydrogen dihedrals: 967 Unresolved non-hydrogen chiralities: 149 Planarities with less than four sites: {'GLN:plan1': 27, 'HIS:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 20, 'ASP:plan': 28, 'PHE:plan': 1, 'GLU:plan': 42, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 542 Chain: "T" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1287 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 15, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "V" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 1726 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 2 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 627 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 257 Chain: "W" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 778 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "X" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 859 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 1 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "Y" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 994 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 9, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 145 Chain: "Z" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 513 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 10, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 278 Chain: "a" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "9" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 160 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 3, 'TRANS': 15} Time building chain proxies: 21.66, per 1000 atoms: 0.44 Number of scatterers: 49460 At special positions: 0 Unit cell: (156.51, 223.11, 390.72, 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 156 16.00 O 8990 8.00 N 9116 7.00 C 31198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS O 75 " - pdb=" SG CYS O 84 " distance=2.03 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 161 " distance=2.03 Simple disulfide: pdb=" SG CYS W 55 " - pdb=" SG CYS W 80 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 9.88 Conformation dependent library (CDL) restraints added in 6.0 seconds 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15014 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 30 sheets defined 51.3% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'E' and resid 3 through 36 removed outlier: 3.703A pdb=" N ASN E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 63 removed outlier: 3.615A pdb=" N VAL E 45 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 134 through 159 Processing helix chain 'E' and resid 174 through 187 removed outlier: 3.553A pdb=" N ALA E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 26 removed outlier: 4.084A pdb=" N LYS A 26 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 4.212A pdb=" N THR A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.586A pdb=" N LEU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 89 removed outlier: 3.734A pdb=" N MET A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.925A pdb=" N LEU A 138 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 171 through 181 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.721A pdb=" N VAL A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 406 through 423 removed outlier: 3.867A pdb=" N ILE A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 removed outlier: 3.598A pdb=" N ALA A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'B' and resid 27 through 52 Processing helix chain 'B' and resid 63 through 141 Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.923A pdb=" N ILE B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.999A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.536A pdb=" N VAL C 104 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 135 removed outlier: 3.968A pdb=" N VAL C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 183 through 188 removed outlier: 3.742A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 25 removed outlier: 3.593A pdb=" N ASP D 23 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 98 Processing helix chain 'D' and resid 103 through 175 removed outlier: 3.665A pdb=" N GLU D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Proline residue: D 128 - end of helix Proline residue: D 172 - end of helix Processing helix chain 'F' and resid 62 through 73 Processing helix chain 'F' and resid 82 through 100 Processing helix chain 'F' and resid 106 through 132 removed outlier: 4.071A pdb=" N GLN F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 27 Processing helix chain 'G' and resid 35 through 58 removed outlier: 4.233A pdb=" N GLN G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 74 removed outlier: 4.101A pdb=" N PHE G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY G 74 " --> pdb=" O TYR G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 117 Processing helix chain 'G' and resid 117 through 127 removed outlier: 3.768A pdb=" N MET G 121 " --> pdb=" O PHE G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 22 removed outlier: 4.160A pdb=" N GLY H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 31 removed outlier: 3.930A pdb=" N THR H 30 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 27 through 31' Processing helix chain 'H' and resid 46 through 51 removed outlier: 3.586A pdb=" N ALA H 50 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 51 " --> pdb=" O ARG H 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 51' Processing helix chain 'H' and resid 53 through 68 Processing helix chain 'H' and resid 86 through 115 Processing helix chain 'I' and resid 57 through 77 Processing helix chain 'I' and resid 78 through 82 removed outlier: 3.661A pdb=" N LYS I 82 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 114 removed outlier: 3.640A pdb=" N ASP I 114 " --> pdb=" O LYS I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 148 Processing helix chain 'I' and resid 149 through 154 removed outlier: 4.082A pdb=" N HIS I 152 " --> pdb=" O ALA I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 169 removed outlier: 4.210A pdb=" N THR I 168 " --> pdb=" O ILE I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 183 removed outlier: 3.882A pdb=" N ILE I 183 " --> pdb=" O ILE I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 195 Processing helix chain 'I' and resid 196 through 212 removed outlier: 4.368A pdb=" N GLN I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 276 No H-bonds generated for 'chain 'I' and resid 274 through 276' Processing helix chain 'I' and resid 277 through 291 removed outlier: 3.695A pdb=" N ASP I 291 " --> pdb=" O ARG I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 325 removed outlier: 3.777A pdb=" N LEU I 302 " --> pdb=" O MET I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 330 removed outlier: 3.606A pdb=" N LEU I 329 " --> pdb=" O TRP I 326 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 330 " --> pdb=" O GLY I 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 326 through 330' Processing helix chain 'I' and resid 388 through 392 removed outlier: 3.904A pdb=" N VAL I 392 " --> pdb=" O SER I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 430 removed outlier: 3.910A pdb=" N LEU I 406 " --> pdb=" O SER I 402 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU I 407 " --> pdb=" O ILE I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 491 removed outlier: 3.825A pdb=" N MET I 484 " --> pdb=" O THR I 480 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 516 Processing helix chain 'I' and resid 601 through 607 Processing helix chain 'I' and resid 644 through 668 removed outlier: 4.016A pdb=" N HIS I 649 " --> pdb=" O LYS I 645 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE I 650 " --> pdb=" O VAL I 646 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP I 655 " --> pdb=" O VAL I 651 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR I 656 " --> pdb=" O ALA I 652 " (cutoff:3.500A) Proline residue: I 659 - end of helix removed outlier: 3.612A pdb=" N GLY I 662 " --> pdb=" O MET I 658 " (cutoff:3.500A) Processing helix chain 'I' and resid 702 through 710 removed outlier: 3.857A pdb=" N ALA I 706 " --> pdb=" O GLU I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 768 through 790 removed outlier: 3.581A pdb=" N ALA I 790 " --> pdb=" O VAL I 786 " (cutoff:3.500A) Processing helix chain 'I' and resid 795 through 799 Processing helix chain 'I' and resid 854 through 868 removed outlier: 4.109A pdb=" N HIS I 859 " --> pdb=" O ASN I 855 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN I 860 " --> pdb=" O THR I 856 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR I 868 " --> pdb=" O MET I 864 " (cutoff:3.500A) Processing helix chain 'I' and resid 870 through 891 removed outlier: 3.535A pdb=" N LEU I 874 " --> pdb=" O ASN I 870 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA I 883 " --> pdb=" O PHE I 879 " (cutoff:3.500A) Proline residue: I 884 - end of helix removed outlier: 3.513A pdb=" N LYS I 890 " --> pdb=" O ASN I 886 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU I 891 " --> pdb=" O ALA I 887 " (cutoff:3.500A) Processing helix chain 'I' and resid 966 through 973 removed outlier: 4.087A pdb=" N VAL I 973 " --> pdb=" O LEU I 969 " (cutoff:3.500A) Processing helix chain 'I' and resid 1186 through 1191 Processing helix chain 'I' and resid 1210 through 1232 removed outlier: 3.863A pdb=" N GLU I1232 " --> pdb=" O ILE I1228 " (cutoff:3.500A) Processing helix chain 'I' and resid 1282 through 1294 Processing helix chain 'I' and resid 1301 through 1310 removed outlier: 4.133A pdb=" N ILE I1305 " --> pdb=" O ALA I1301 " (cutoff:3.500A) Processing helix chain 'I' and resid 1315 through 1330 removed outlier: 3.975A pdb=" N ARG I1319 " --> pdb=" O THR I1315 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP I1320 " --> pdb=" O HIS I1316 " (cutoff:3.500A) Processing helix chain 'I' and resid 1412 through 1426 Proline residue: I1417 - end of helix removed outlier: 3.509A pdb=" N ARG I1426 " --> pdb=" O ASN I1422 " (cutoff:3.500A) Processing helix chain 'I' and resid 1439 through 1447 Processing helix chain 'J' and resid 622 through 630 removed outlier: 3.946A pdb=" N VAL J 626 " --> pdb=" O LEU J 622 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU J 627 " --> pdb=" O LEU J 623 " (cutoff:3.500A) Processing helix chain 'J' and resid 637 through 651 removed outlier: 4.348A pdb=" N ARG J 641 " --> pdb=" O HIS J 637 " (cutoff:3.500A) Proline residue: J 645 - end of helix Processing helix chain 'J' and resid 677 through 684 Processing helix chain 'J' and resid 739 through 745 removed outlier: 3.578A pdb=" N GLN J 743 " --> pdb=" O ASP J 739 " (cutoff:3.500A) Processing helix chain 'J' and resid 747 through 764 Processing helix chain 'J' and resid 771 through 784 Processing helix chain 'K' and resid 132 through 137 Processing helix chain 'K' and resid 194 through 198 removed outlier: 4.028A pdb=" N ARG K 198 " --> pdb=" O CYS K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 258 removed outlier: 3.877A pdb=" N THR K 256 " --> pdb=" O MET K 253 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP K 258 " --> pdb=" O CYS K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 472 Processing helix chain 'K' and resid 483 through 501 removed outlier: 3.967A pdb=" N VAL K 487 " --> pdb=" O GLN K 483 " (cutoff:3.500A) Processing helix chain 'K' and resid 505 through 523 removed outlier: 6.907A pdb=" N THR K 511 " --> pdb=" O GLN K 507 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG K 512 " --> pdb=" O VAL K 508 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE K 513 " --> pdb=" O LEU K 509 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU K 523 " --> pdb=" O SER K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 531 through 552 removed outlier: 4.326A pdb=" N HIS K 535 " --> pdb=" O VAL K 531 " (cutoff:3.500A) Processing helix chain 'K' and resid 563 through 570 removed outlier: 3.716A pdb=" N ILE K 570 " --> pdb=" O ARG K 566 " (cutoff:3.500A) Processing helix chain 'K' and resid 571 through 573 No H-bonds generated for 'chain 'K' and resid 571 through 573' Processing helix chain 'K' and resid 578 through 587 removed outlier: 3.557A pdb=" N VAL K 582 " --> pdb=" O ASP K 578 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE K 584 " --> pdb=" O ASP K 580 " (cutoff:3.500A) Processing helix chain 'K' and resid 605 through 619 removed outlier: 3.678A pdb=" N GLY K 609 " --> pdb=" O LEU K 605 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL K 617 " --> pdb=" O LEU K 613 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 656 Processing helix chain 'K' and resid 672 through 688 Processing helix chain 'K' and resid 721 through 727 removed outlier: 3.722A pdb=" N LEU K 725 " --> pdb=" O ALA K 721 " (cutoff:3.500A) Processing helix chain 'K' and resid 803 through 810 removed outlier: 3.857A pdb=" N GLU K 807 " --> pdb=" O VAL K 803 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 40 Processing helix chain 'L' and resid 92 through 118 Processing helix chain 'L' and resid 141 through 167 Processing helix chain 'L' and resid 170 through 175 removed outlier: 3.549A pdb=" N GLU L 174 " --> pdb=" O ALA L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 193 Processing helix chain 'L' and resid 287 through 311 removed outlier: 3.625A pdb=" N ARG L 311 " --> pdb=" O ALA L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 368 through 383 removed outlier: 3.686A pdb=" N ASN L 372 " --> pdb=" O VAL L 368 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU L 376 " --> pdb=" O ASN L 372 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE L 377 " --> pdb=" O LEU L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 407 removed outlier: 4.336A pdb=" N GLY L 407 " --> pdb=" O MET L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 419 Processing helix chain 'L' and resid 424 through 452 removed outlier: 3.653A pdb=" N LYS L 428 " --> pdb=" O GLY L 424 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA L 433 " --> pdb=" O ILE L 429 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE L 446 " --> pdb=" O THR L 442 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU L 449 " --> pdb=" O THR L 445 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 539 removed outlier: 3.899A pdb=" N PHE L 522 " --> pdb=" O GLU L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 603 through 608 removed outlier: 4.321A pdb=" N LEU L 608 " --> pdb=" O LYS L 604 " (cutoff:3.500A) Processing helix chain 'L' and resid 635 through 641 removed outlier: 4.268A pdb=" N LEU L 639 " --> pdb=" O TYR L 635 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 41 removed outlier: 3.596A pdb=" N ARG M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY M 41 " --> pdb=" O HIS M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 121 Processing helix chain 'M' and resid 181 through 193 removed outlier: 3.834A pdb=" N ASP M 185 " --> pdb=" O MET M 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 32 Processing helix chain 'O' and resid 87 through 98 removed outlier: 3.570A pdb=" N PHE O 91 " --> pdb=" O ALA O 87 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU O 94 " --> pdb=" O ASN O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 165 removed outlier: 3.860A pdb=" N LEU O 157 " --> pdb=" O CYS O 153 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU O 158 " --> pdb=" O TRP O 154 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU O 159 " --> pdb=" O SER O 155 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU O 161 " --> pdb=" O LEU O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 199 removed outlier: 3.769A pdb=" N GLN O 192 " --> pdb=" O ASP O 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 27 removed outlier: 3.945A pdb=" N GLN P 7 " --> pdb=" O ASP P 3 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN P 27 " --> pdb=" O ILE P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 74 Processing helix chain 'P' and resid 83 through 133 Processing helix chain 'Q' and resid 11 through 32 Processing helix chain 'Q' and resid 55 through 60 removed outlier: 4.130A pdb=" N TYR Q 59 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 73 removed outlier: 3.754A pdb=" N ARG Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA Q 71 " --> pdb=" O ASN Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 87 removed outlier: 3.663A pdb=" N LEU Q 78 " --> pdb=" O SER Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 137 removed outlier: 3.928A pdb=" N CYS Q 112 " --> pdb=" O LEU Q 108 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU Q 132 " --> pdb=" O TYR Q 128 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU Q 133 " --> pdb=" O GLU Q 129 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER Q 137 " --> pdb=" O GLU Q 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 14 Processing helix chain 'R' and resid 35 through 51 removed outlier: 3.650A pdb=" N LEU R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 69 removed outlier: 4.217A pdb=" N CYS R 59 " --> pdb=" O SER R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 90 Processing helix chain 'R' and resid 93 through 102 removed outlier: 3.570A pdb=" N VAL R 97 " --> pdb=" O PRO R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 125 Processing helix chain 'R' and resid 126 through 128 No H-bonds generated for 'chain 'R' and resid 126 through 128' Processing helix chain 'R' and resid 134 through 147 removed outlier: 3.805A pdb=" N LEU R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR R 147 " --> pdb=" O GLU R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 174 removed outlier: 3.609A pdb=" N ALA R 162 " --> pdb=" O GLN R 158 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA R 163 " --> pdb=" O GLN R 159 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 187 through 190 Processing helix chain 'R' and resid 205 through 211 Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.895A pdb=" N ALA R 216 " --> pdb=" O PHE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 263 Processing helix chain 'R' and resid 266 through 275 Processing helix chain 'R' and resid 278 through 287 removed outlier: 4.457A pdb=" N MET R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 317 removed outlier: 4.232A pdb=" N GLN R 303 " --> pdb=" O VAL R 299 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU R 304 " --> pdb=" O LEU R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 324 removed outlier: 3.750A pdb=" N PHE R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP R 323 " --> pdb=" O GLU R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 341 removed outlier: 3.718A pdb=" N LEU R 330 " --> pdb=" O THR R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 360 Processing helix chain 'R' and resid 367 through 382 removed outlier: 4.375A pdb=" N HIS R 371 " --> pdb=" O LYS R 367 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY R 382 " --> pdb=" O GLN R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 403 removed outlier: 3.875A pdb=" N PHE R 392 " --> pdb=" O ALA R 388 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 419 through 440 removed outlier: 5.006A pdb=" N MET R 425 " --> pdb=" O HIS R 421 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR R 426 " --> pdb=" O ALA R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 441 through 445 Processing helix chain 'R' and resid 448 through 450 No H-bonds generated for 'chain 'R' and resid 448 through 450' Processing helix chain 'R' and resid 451 through 456 removed outlier: 3.513A pdb=" N GLU R 456 " --> pdb=" O LYS R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 489 through 494 removed outlier: 3.720A pdb=" N GLY R 493 " --> pdb=" O THR R 489 " (cutoff:3.500A) Processing helix chain 'R' and resid 541 through 554 removed outlier: 3.549A pdb=" N ARG R 546 " --> pdb=" O SER R 542 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR R 553 " --> pdb=" O LYS R 549 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS R 554 " --> pdb=" O LEU R 550 " (cutoff:3.500A) Processing helix chain 'R' and resid 563 through 569 removed outlier: 3.632A pdb=" N TYR R 567 " --> pdb=" O LEU R 563 " (cutoff:3.500A) Processing helix chain 'R' and resid 570 through 577 removed outlier: 3.747A pdb=" N MET R 574 " --> pdb=" O LEU R 570 " (cutoff:3.500A) Processing helix chain 'R' and resid 577 through 589 Processing helix chain 'R' and resid 590 through 595 Processing helix chain 'R' and resid 600 through 612 removed outlier: 3.682A pdb=" N LEU R 604 " --> pdb=" O ILE R 600 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU R 606 " --> pdb=" O HIS R 602 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N MET R 607 " --> pdb=" O THR R 603 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER R 609 " --> pdb=" O LEU R 605 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET R 612 " --> pdb=" O PHE R 608 " (cutoff:3.500A) Processing helix chain 'R' and resid 616 through 633 Processing helix chain 'R' and resid 639 through 641 No H-bonds generated for 'chain 'R' and resid 639 through 641' Processing helix chain 'R' and resid 642 through 655 removed outlier: 3.512A pdb=" N SER R 647 " --> pdb=" O LEU R 643 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG R 651 " --> pdb=" O SER R 647 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU R 652 " --> pdb=" O THR R 648 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE R 653 " --> pdb=" O ALA R 649 " (cutoff:3.500A) Processing helix chain 'R' and resid 662 through 669 removed outlier: 4.231A pdb=" N THR R 666 " --> pdb=" O PRO R 663 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE R 668 " --> pdb=" O PHE R 665 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU R 669 " --> pdb=" O THR R 666 " (cutoff:3.500A) Processing helix chain 'R' and resid 670 through 675 Processing helix chain 'R' and resid 680 through 696 Processing helix chain 'R' and resid 709 through 723 removed outlier: 3.753A pdb=" N ASP R 714 " --> pdb=" O THR R 710 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE R 715 " --> pdb=" O TRP R 711 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR R 718 " --> pdb=" O ASP R 714 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE R 722 " --> pdb=" O THR R 718 " (cutoff:3.500A) Processing helix chain 'R' and resid 739 through 743 Processing helix chain 'R' and resid 744 through 753 removed outlier: 4.015A pdb=" N ASN R 747 " --> pdb=" O LYS R 744 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL R 748 " --> pdb=" O GLN R 745 " (cutoff:3.500A) Proline residue: R 749 - end of helix Processing helix chain 'R' and resid 754 through 771 removed outlier: 3.862A pdb=" N LYS R 758 " --> pdb=" O PHE R 754 " (cutoff:3.500A) Processing helix chain 'R' and resid 773 through 781 removed outlier: 4.786A pdb=" N GLN R 779 " --> pdb=" O GLU R 775 " (cutoff:3.500A) Processing helix chain 'R' and resid 785 through 790 removed outlier: 3.936A pdb=" N LEU R 790 " --> pdb=" O PRO R 786 " (cutoff:3.500A) Processing helix chain 'R' and resid 790 through 796 removed outlier: 4.110A pdb=" N TRP R 794 " --> pdb=" O LEU R 790 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS R 795 " --> pdb=" O CYS R 791 " (cutoff:3.500A) Processing helix chain 'R' and resid 805 through 814 removed outlier: 4.401A pdb=" N LYS R 809 " --> pdb=" O GLN R 805 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL R 810 " --> pdb=" O ILE R 806 " (cutoff:3.500A) Processing helix chain 'R' and resid 818 through 838 removed outlier: 4.414A pdb=" N ALA R 838 " --> pdb=" O PHE R 834 " (cutoff:3.500A) Processing helix chain 'R' and resid 842 through 854 removed outlier: 5.186A pdb=" N ASN R 851 " --> pdb=" O ILE R 847 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASP R 852 " --> pdb=" O GLU R 848 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL R 854 " --> pdb=" O LEU R 850 " (cutoff:3.500A) Processing helix chain 'R' and resid 864 through 874 removed outlier: 3.800A pdb=" N CYS R 868 " --> pdb=" O ARG R 864 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG R 872 " --> pdb=" O CYS R 868 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS R 874 " --> pdb=" O ALA R 870 " (cutoff:3.500A) Processing helix chain 'R' and resid 881 through 892 Processing helix chain 'R' and resid 896 through 903 removed outlier: 3.572A pdb=" N VAL R 900 " --> pdb=" O PHE R 896 " (cutoff:3.500A) Processing helix chain 'R' and resid 916 through 928 Processing helix chain 'R' and resid 958 through 972 removed outlier: 4.266A pdb=" N ARG R 962 " --> pdb=" O ASN R 958 " (cutoff:3.500A) Proline residue: R 965 - end of helix Processing helix chain 'R' and resid 979 through 992 removed outlier: 3.529A pdb=" N SER R 983 " --> pdb=" O PRO R 979 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR R 986 " --> pdb=" O LYS R 982 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU R 988 " --> pdb=" O LEU R 984 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP R 989 " --> pdb=" O GLU R 985 " (cutoff:3.500A) Processing helix chain 'R' and resid 993 through 996 Processing helix chain 'R' and resid 1000 through 1006 removed outlier: 3.665A pdb=" N TYR R1004 " --> pdb=" O ARG R1000 " (cutoff:3.500A) Processing helix chain 'R' and resid 1007 through 1010 removed outlier: 3.596A pdb=" N HIS R1010 " --> pdb=" O ASN R1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1007 through 1010' Processing helix chain 'R' and resid 1012 through 1036 removed outlier: 3.673A pdb=" N ARG R1017 " --> pdb=" O GLU R1013 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASN R1018 " --> pdb=" O MET R1014 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARG R1019 " --> pdb=" O CYS R1015 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU R1022 " --> pdb=" O ASN R1018 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS R1025 " --> pdb=" O HIS R1021 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS R1028 " --> pdb=" O ARG R1024 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY R1032 " --> pdb=" O HIS R1028 " (cutoff:3.500A) Processing helix chain 'R' and resid 1044 through 1051 removed outlier: 4.000A pdb=" N TYR R1048 " --> pdb=" O LEU R1044 " (cutoff:3.500A) Processing helix chain 'R' and resid 1063 through 1077 Processing helix chain 'R' and resid 1099 through 1107 removed outlier: 3.768A pdb=" N LEU R1105 " --> pdb=" O ALA R1102 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL R1107 " --> pdb=" O ALA R1104 " (cutoff:3.500A) Processing helix chain 'R' and resid 1120 through 1132 removed outlier: 4.452A pdb=" N VAL R1129 " --> pdb=" O ALA R1125 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL R1130 " --> pdb=" O LEU R1126 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU R1131 " --> pdb=" O LEU R1127 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS R1132 " --> pdb=" O ASN R1128 " (cutoff:3.500A) Processing helix chain 'R' and resid 1141 through 1154 Processing helix chain 'R' and resid 1157 through 1172 removed outlier: 3.767A pdb=" N TRP R1161 " --> pdb=" O PRO R1157 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU R1164 " --> pdb=" O TYR R1160 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS R1165 " --> pdb=" O TRP R1161 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL R1171 " --> pdb=" O ARG R1167 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE R1172 " --> pdb=" O ILE R1168 " (cutoff:3.500A) Processing helix chain 'R' and resid 1186 through 1192 removed outlier: 3.807A pdb=" N LEU R1190 " --> pdb=" O TYR R1186 " (cutoff:3.500A) Processing helix chain 'R' and resid 1194 through 1198 Processing helix chain 'R' and resid 1203 through 1217 Processing helix chain 'R' and resid 1222 through 1224 No H-bonds generated for 'chain 'R' and resid 1222 through 1224' Processing helix chain 'R' and resid 1225 through 1233 removed outlier: 4.784A pdb=" N LYS R1229 " --> pdb=" O SER R1225 " (cutoff:3.500A) Processing helix chain 'R' and resid 1235 through 1239 removed outlier: 4.075A pdb=" N VAL R1238 " --> pdb=" O LEU R1235 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL R1239 " --> pdb=" O LEU R1236 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1235 through 1239' Processing helix chain 'R' and resid 1242 through 1253 Processing helix chain 'R' and resid 1255 through 1262 removed outlier: 3.816A pdb=" N PHE R1259 " --> pdb=" O PHE R1255 " (cutoff:3.500A) Processing helix chain 'R' and resid 1263 through 1284 removed outlier: 3.649A pdb=" N MET R1267 " --> pdb=" O ARG R1263 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE R1268 " --> pdb=" O THR R1264 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU R1269 " --> pdb=" O ARG R1265 " (cutoff:3.500A) Processing helix chain 'R' and resid 1290 through 1305 removed outlier: 3.610A pdb=" N ILE R1294 " --> pdb=" O TYR R1290 " (cutoff:3.500A) Processing helix chain 'R' and resid 1310 through 1319 removed outlier: 3.520A pdb=" N GLU R1315 " --> pdb=" O LYS R1311 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS R1316 " --> pdb=" O GLU R1312 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE R1317 " --> pdb=" O GLN R1313 " (cutoff:3.500A) Processing helix chain 'R' and resid 1322 through 1329 Processing helix chain 'R' and resid 1330 through 1334 removed outlier: 3.525A pdb=" N HIS R1334 " --> pdb=" O PHE R1331 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 16 Processing helix chain 'S' and resid 22 through 31 removed outlier: 3.521A pdb=" N ASN S 26 " --> pdb=" O GLN S 22 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 40 removed outlier: 3.813A pdb=" N ILE S 39 " --> pdb=" O THR S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 51 removed outlier: 3.615A pdb=" N GLN S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET S 51 " --> pdb=" O LEU S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 68 removed outlier: 3.870A pdb=" N LEU S 64 " --> pdb=" O ILE S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 83 Processing helix chain 'S' and resid 84 through 89 removed outlier: 3.811A pdb=" N PHE S 88 " --> pdb=" O LYS S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 106 removed outlier: 3.501A pdb=" N ALA S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 133 removed outlier: 3.641A pdb=" N GLY S 119 " --> pdb=" O GLU S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 134 through 139 Processing helix chain 'S' and resid 156 through 169 Processing helix chain 'S' and resid 174 through 183 Processing helix chain 'S' and resid 186 through 203 Processing helix chain 'S' and resid 213 through 225 removed outlier: 3.619A pdb=" N ARG S 217 " --> pdb=" O SER S 213 " (cutoff:3.500A) Processing helix chain 'S' and resid 241 through 255 removed outlier: 4.124A pdb=" N HIS S 245 " --> pdb=" O PHE S 241 " (cutoff:3.500A) Processing helix chain 'S' and resid 261 through 273 removed outlier: 3.722A pdb=" N GLU S 265 " --> pdb=" O GLN S 261 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 292 Processing helix chain 'S' and resid 299 through 323 removed outlier: 4.061A pdb=" N LEU S 303 " --> pdb=" O GLY S 299 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE S 313 " --> pdb=" O THR S 309 " (cutoff:3.500A) Proline residue: S 314 - end of helix Processing helix chain 'S' and resid 332 through 342 Processing helix chain 'S' and resid 344 through 356 removed outlier: 3.568A pdb=" N LEU S 348 " --> pdb=" O LEU S 344 " (cutoff:3.500A) Processing helix chain 'S' and resid 357 through 373 Processing helix chain 'S' and resid 378 through 393 removed outlier: 3.545A pdb=" N ASP S 388 " --> pdb=" O LYS S 384 " (cutoff:3.500A) Proline residue: S 391 - end of helix Processing helix chain 'S' and resid 411 through 425 removed outlier: 4.658A pdb=" N THR S 421 " --> pdb=" O ASN S 417 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET S 422 " --> pdb=" O ILE S 418 " (cutoff:3.500A) Processing helix chain 'S' and resid 436 through 445 removed outlier: 4.630A pdb=" N SER S 442 " --> pdb=" O GLY S 438 " (cutoff:3.500A) Processing helix chain 'S' and resid 447 through 454 Processing helix chain 'S' and resid 458 through 473 Processing helix chain 'S' and resid 480 through 505 Processing helix chain 'S' and resid 506 through 514 Processing helix chain 'S' and resid 537 through 542 Processing helix chain 'S' and resid 552 through 560 Processing helix chain 'S' and resid 578 through 590 removed outlier: 3.819A pdb=" N TRP S 590 " --> pdb=" O ILE S 586 " (cutoff:3.500A) Processing helix chain 'S' and resid 597 through 607 removed outlier: 3.518A pdb=" N GLN S 601 " --> pdb=" O PHE S 597 " (cutoff:3.500A) Processing helix chain 'S' and resid 612 through 626 Processing helix chain 'S' and resid 633 through 643 removed outlier: 3.510A pdb=" N SER S 637 " --> pdb=" O GLU S 633 " (cutoff:3.500A) Processing helix chain 'S' and resid 657 through 672 Processing helix chain 'S' and resid 675 through 680 Processing helix chain 'S' and resid 707 through 719 removed outlier: 5.273A pdb=" N ALA S 714 " --> pdb=" O THR S 710 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS S 715 " --> pdb=" O ASP S 711 " (cutoff:3.500A) Processing helix chain 'S' and resid 723 through 735 removed outlier: 3.527A pdb=" N HIS S 728 " --> pdb=" O SER S 724 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE S 729 " --> pdb=" O ARG S 725 " (cutoff:3.500A) Processing helix chain 'S' and resid 738 through 751 removed outlier: 3.593A pdb=" N LEU S 751 " --> pdb=" O ILE S 747 " (cutoff:3.500A) Processing helix chain 'S' and resid 755 through 770 removed outlier: 3.629A pdb=" N SER S 768 " --> pdb=" O GLN S 764 " (cutoff:3.500A) Processing helix chain 'S' and resid 773 through 785 Processing helix chain 'S' and resid 786 through 791 Processing helix chain 'S' and resid 795 through 800 removed outlier: 3.828A pdb=" N LEU S 799 " --> pdb=" O LYS S 795 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET S 800 " --> pdb=" O TRP S 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 795 through 800' Processing helix chain 'S' and resid 802 through 820 removed outlier: 3.912A pdb=" N ALA S 806 " --> pdb=" O PRO S 802 " (cutoff:3.500A) Processing helix chain 'S' and resid 826 through 831 Processing helix chain 'S' and resid 893 through 910 Processing helix chain 'S' and resid 917 through 930 Processing helix chain 'S' and resid 945 through 954 Processing helix chain 'S' and resid 962 through 968 Processing helix chain 'S' and resid 975 through 985 removed outlier: 4.105A pdb=" N VAL S 979 " --> pdb=" O LEU S 975 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA S 985 " --> pdb=" O ALA S 981 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 37 removed outlier: 4.207A pdb=" N PHE T 32 " --> pdb=" O LEU T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 45 Processing helix chain 'T' and resid 46 through 48 No H-bonds generated for 'chain 'T' and resid 46 through 48' Processing helix chain 'T' and resid 88 through 91 Processing helix chain 'T' and resid 92 through 101 Processing helix chain 'T' and resid 115 through 132 removed outlier: 3.596A pdb=" N SER T 119 " --> pdb=" O ALA T 115 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS T 130 " --> pdb=" O ASP T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 174 Processing helix chain 'T' and resid 193 through 197 Processing helix chain 'V' and resid 10 through 36 removed outlier: 3.830A pdb=" N PHE V 14 " --> pdb=" O ASN V 10 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER V 15 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN V 16 " --> pdb=" O GLU V 12 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL V 28 " --> pdb=" O LEU V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 72 removed outlier: 3.962A pdb=" N LYS V 50 " --> pdb=" O GLU V 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN V 59 " --> pdb=" O ASN V 55 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU V 60 " --> pdb=" O PHE V 56 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS V 61 " --> pdb=" O GLN V 57 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER V 62 " --> pdb=" O ASP V 58 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL V 63 " --> pdb=" O ASN V 59 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU V 69 " --> pdb=" O ARG V 65 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU V 70 " --> pdb=" O ASP V 66 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU V 71 " --> pdb=" O LEU V 67 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG V 72 " --> pdb=" O ASN V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 84 removed outlier: 4.367A pdb=" N ASN V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 90 Processing helix chain 'V' and resid 91 through 95 Processing helix chain 'V' and resid 105 through 128 removed outlier: 3.586A pdb=" N ASN V 115 " --> pdb=" O TYR V 111 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY V 126 " --> pdb=" O GLY V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 161 through 172 Processing helix chain 'V' and resid 239 through 253 Processing helix chain 'V' and resid 258 through 272 removed outlier: 3.507A pdb=" N SER V 272 " --> pdb=" O THR V 268 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 55 removed outlier: 4.228A pdb=" N GLU W 49 " --> pdb=" O VAL W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 106 removed outlier: 4.445A pdb=" N GLY W 76 " --> pdb=" O GLU W 72 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL W 77 " --> pdb=" O ILE W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 143 removed outlier: 3.939A pdb=" N VAL W 110 " --> pdb=" O LYS W 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 89 removed outlier: 3.942A pdb=" N ARG X 58 " --> pdb=" O ASP X 54 " (cutoff:3.500A) Proline residue: X 64 - end of helix removed outlier: 4.145A pdb=" N ASN X 89 " --> pdb=" O THR X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 136 removed outlier: 3.614A pdb=" N LEU X 105 " --> pdb=" O PHE X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 185 Processing helix chain 'Y' and resid 29 through 57 removed outlier: 4.066A pdb=" N ASN Y 57 " --> pdb=" O GLN Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 102 removed outlier: 3.903A pdb=" N ASP Y 73 " --> pdb=" O GLY Y 69 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS Y 98 " --> pdb=" O LEU Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 119 Proline residue: Y 116 - end of helix Processing helix chain 'Y' and resid 139 through 166 removed outlier: 4.212A pdb=" N GLN Y 162 " --> pdb=" O GLN Y 158 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU Y 163 " --> pdb=" O ILE Y 159 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 15 Processing helix chain 'Z' and resid 21 through 29 Processing helix chain 'Z' and resid 30 through 34 removed outlier: 3.581A pdb=" N LEU Z 34 " --> pdb=" O PRO Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 54 removed outlier: 3.627A pdb=" N VAL Z 49 " --> pdb=" O ASP Z 45 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR Z 51 " --> pdb=" O ALA Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 79 removed outlier: 3.966A pdb=" N MET Z 75 " --> pdb=" O GLN Z 71 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU Z 76 " --> pdb=" O CYS Z 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 82 No H-bonds generated for 'chain 'Z' and resid 80 through 82' Processing helix chain 'Z' and resid 90 through 103 removed outlier: 3.507A pdb=" N ALA Z 94 " --> pdb=" O ASN Z 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 18 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.792A pdb=" N MET A 222 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 367 Processing sheet with id=AA5, first strand: chain 'A' and resid 441 through 442 removed outlier: 4.167A pdb=" N GLU A 441 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 453 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 70 removed outlier: 3.516A pdb=" N GLU C 67 " --> pdb=" O GLN C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 332 through 333 Processing sheet with id=AA8, first strand: chain 'I' and resid 438 through 439 removed outlier: 3.732A pdb=" N GLU I 438 " --> pdb=" O ILE I 445 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE I 445 " --> pdb=" O GLU I 438 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 459 through 460 removed outlier: 3.607A pdb=" N HIS I 459 " --> pdb=" O MET I 472 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 521 through 523 removed outlier: 3.559A pdb=" N ILE I 521 " --> pdb=" O LEU I 544 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN I 542 " --> pdb=" O THR I 523 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 677 through 678 removed outlier: 8.969A pdb=" N HIS I 686 " --> pdb=" O LEU I 718 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU I 718 " --> pdb=" O HIS I 686 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE I 688 " --> pdb=" O PHE I 716 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP I 713 " --> pdb=" O VAL I 731 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 829 through 830 removed outlier: 3.887A pdb=" N GLN I 829 " --> pdb=" O HIS I 838 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 919 through 920 removed outlier: 3.790A pdb=" N ILE I 920 " --> pdb=" O ILE I 932 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 1340 through 1341 removed outlier: 3.669A pdb=" N ASN I1340 " --> pdb=" O GLN I1376 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU I1369 " --> pdb=" O TYR I1394 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TYR I1394 " --> pdb=" O LEU I1369 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE I1371 " --> pdb=" O ILE I1392 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE I1392 " --> pdb=" O PHE I1371 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 692 through 694 Processing sheet with id=AB7, first strand: chain 'K' and resid 50 through 52 Processing sheet with id=AB8, first strand: chain 'K' and resid 129 through 130 Processing sheet with id=AB9, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AC1, first strand: chain 'K' and resid 282 through 283 removed outlier: 6.952A pdb=" N VAL K 294 " --> pdb=" O ALA K 332 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA K 332 " --> pdb=" O VAL K 294 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS K 296 " --> pdb=" O LEU K 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'L' and resid 461 through 462 removed outlier: 4.223A pdb=" N SER L 471 " --> pdb=" O ASN L 494 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 567 through 571 Processing sheet with id=AC5, first strand: chain 'M' and resid 25 through 27 removed outlier: 3.543A pdb=" N VAL M 27 " --> pdb=" O TYR M 167 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR M 167 " --> pdb=" O VAL M 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 25 through 27 removed outlier: 3.543A pdb=" N VAL M 27 " --> pdb=" O TYR M 167 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR M 167 " --> pdb=" O VAL M 27 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL M 173 " --> pdb=" O TYR M 21 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET M 18 " --> pdb=" O ASN M 104 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA M 100 " --> pdb=" O LEU M 22 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS M 105 " --> pdb=" O TYR M 87 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU M 85 " --> pdb=" O ASP M 107 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'M' and resid 58 through 59 Processing sheet with id=AC9, first strand: chain 'O' and resid 35 through 41 removed outlier: 3.793A pdb=" N GLY O 37 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR O 115 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL O 126 " --> pdb=" O THR O 115 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 45 through 46 removed outlier: 3.554A pdb=" N LEU O 62 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 68 through 69 removed outlier: 3.576A pdb=" N SER T 181 " --> pdb=" O CYS T 142 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 178 through 180 2726 hydrogen bonds defined for protein. 7929 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: 16.45 Time building geometry restraints manager: 11.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 17267 1.34 - 1.46: 10830 1.46 - 1.58: 21990 1.58 - 1.70: 0 1.70 - 1.81: 229 Bond restraints: 50316 Sorted by residual: bond pdb=" CD GLN Y 20 " pdb=" NE2 GLN Y 20 " ideal model delta sigma weight residual 1.328 1.249 0.079 2.10e-02 2.27e+03 1.42e+01 bond pdb=" N PRO C 168 " pdb=" CD PRO C 168 " ideal model delta sigma weight residual 1.473 1.512 -0.039 1.40e-02 5.10e+03 7.73e+00 bond pdb=" C PHE R 250 " pdb=" N PRO R 251 " ideal model delta sigma weight residual 1.331 1.365 -0.034 1.21e-02 6.83e+03 7.68e+00 bond pdb=" C PRO R 786 " pdb=" N PRO R 787 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.54e+00 bond pdb=" C LEU R 978 " pdb=" N PRO R 979 " ideal model delta sigma weight residual 1.336 1.363 -0.028 1.08e-02 8.57e+03 6.57e+00 ... (remaining 50311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 68598 3.01 - 6.02: 599 6.02 - 9.03: 42 9.03 - 12.04: 1 12.04 - 15.05: 2 Bond angle restraints: 69242 Sorted by residual: angle pdb=" CA PRO C 168 " pdb=" N PRO C 168 " pdb=" CD PRO C 168 " ideal model delta sigma weight residual 112.00 99.97 12.03 1.40e+00 5.10e-01 7.38e+01 angle pdb=" C ALA K 286 " pdb=" N THR K 290 " pdb=" CA THR K 290 " ideal model delta sigma weight residual 121.70 136.75 -15.05 1.80e+00 3.09e-01 6.99e+01 angle pdb=" N PRO I 385 " pdb=" CA PRO I 385 " pdb=" CB PRO I 385 " ideal model delta sigma weight residual 102.88 110.62 -7.74 1.09e+00 8.42e-01 5.05e+01 angle pdb=" N PRO L 92 " pdb=" CA PRO L 92 " pdb=" CB PRO L 92 " ideal model delta sigma weight residual 103.25 110.54 -7.29 1.05e+00 9.07e-01 4.83e+01 angle pdb=" N TYR H 84 " pdb=" CA TYR H 84 " pdb=" C TYR H 84 " ideal model delta sigma weight residual 108.19 115.66 -7.47 1.29e+00 6.01e-01 3.35e+01 ... (remaining 69237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 27866 17.94 - 35.87: 1408 35.87 - 53.81: 247 53.81 - 71.74: 41 71.74 - 89.68: 20 Dihedral angle restraints: 29582 sinusoidal: 6684 harmonic: 22898 Sorted by residual: dihedral pdb=" CA SER H 82 " pdb=" C SER H 82 " pdb=" N SER H 83 " pdb=" CA SER H 83 " ideal model delta harmonic sigma weight residual 180.00 143.26 36.74 0 5.00e+00 4.00e-02 5.40e+01 dihedral pdb=" CB CYS W 55 " pdb=" SG CYS W 55 " pdb=" SG CYS W 80 " pdb=" CB CYS W 80 " ideal model delta sinusoidal sigma weight residual 93.00 32.46 60.54 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CA SER H 85 " pdb=" C SER H 85 " pdb=" N SER H 86 " pdb=" CA SER H 86 " ideal model delta harmonic sigma weight residual -180.00 -146.03 -33.97 0 5.00e+00 4.00e-02 4.61e+01 ... (remaining 29579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 6499 0.044 - 0.088: 1669 0.088 - 0.132: 337 0.132 - 0.175: 20 0.175 - 0.219: 3 Chirality restraints: 8528 Sorted by residual: chirality pdb=" CA PRO L 92 " pdb=" N PRO L 92 " pdb=" C PRO L 92 " pdb=" CB PRO L 92 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO I 385 " pdb=" N PRO I 385 " pdb=" C PRO I 385 " pdb=" CB PRO I 385 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA THR K 290 " pdb=" N THR K 290 " pdb=" C THR K 290 " pdb=" CB THR K 290 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 8525 not shown) Planarity restraints: 9242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 396 " 0.049 5.00e-02 4.00e+02 7.47e-02 8.94e+00 pdb=" N PRO L 397 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO L 397 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO L 397 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN T 209 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO T 210 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO T 210 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO T 210 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO S 802 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO S 803 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO S 803 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 803 " 0.033 5.00e-02 4.00e+02 ... (remaining 9239 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1784 2.71 - 3.26: 53123 3.26 - 3.80: 74871 3.80 - 4.35: 82084 4.35 - 4.90: 132587 Nonbonded interactions: 344449 Sorted by model distance: nonbonded pdb=" OG1 THR S 243 " pdb=" OE1 GLN S 764 " model vdw 2.161 3.040 nonbonded pdb=" O THR L 442 " pdb=" OG1 THR L 445 " model vdw 2.177 3.040 nonbonded pdb=" O ARG H 96 " pdb=" OH TYR L 367 " model vdw 2.182 3.040 nonbonded pdb=" O ASN V 59 " pdb=" OG SER V 62 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR R 808 " pdb=" O TYR R 933 " model vdw 2.193 3.040 ... (remaining 344444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.40 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: 11.780 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: 0.030 Extract box with map and model: 1.490 Check model and map are aligned: 0.290 Set scattering table: 0.340 Process input model: 87.710 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.190 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.003 0.079 50316 Z= 0.189 Angle : 0.796 15.050 69242 Z= 0.511 Chirality : 0.039 0.219 8528 Planarity : 0.004 0.075 9242 Dihedral : 12.129 89.676 14559 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.43 % Favored : 88.48 % Rotamer: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -3.93 (0.09), residues: 7647 helix: -0.59 (0.08), residues: 3498 sheet: -3.96 (0.20), residues: 367 loop : -4.70 (0.08), residues: 3782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 231 HIS 0.008 0.001 HIS K 535 PHE 0.025 0.001 PHE I 643 TYR 0.012 0.001 TYR X 109 ARG 0.002 0.000 ARG J 663 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 841 time to evaluate : 4.268 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 TYR cc_start: 0.7538 (t80) cc_final: 0.6484 (m-10) REVERT: I 307 LEU cc_start: 0.9504 (mm) cc_final: 0.9264 (pp) REVERT: I 312 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8555 (mm-30) REVERT: I 409 ASP cc_start: 0.8735 (t0) cc_final: 0.8527 (t0) REVERT: I 512 LYS cc_start: 0.9483 (ttmt) cc_final: 0.9193 (mtpp) REVERT: I 577 MET cc_start: 0.8585 (ppp) cc_final: 0.8373 (ppp) REVERT: I 650 PHE cc_start: 0.8659 (m-10) cc_final: 0.8457 (m-80) REVERT: I 675 GLN cc_start: 0.8658 (pp30) cc_final: 0.8420 (pp30) REVERT: I 691 LEU cc_start: 0.7746 (tp) cc_final: 0.7432 (mp) REVERT: I 729 GLU cc_start: 0.7697 (tt0) cc_final: 0.7151 (tp30) REVERT: I 896 MET cc_start: 0.8730 (pmm) cc_final: 0.8323 (pmm) REVERT: I 922 LEU cc_start: 0.8652 (tp) cc_final: 0.8355 (tp) REVERT: I 1214 ARG cc_start: 0.9243 (ptt-90) cc_final: 0.8979 (ptp90) REVERT: J 647 MET cc_start: 0.9004 (tpp) cc_final: 0.8681 (tpp) REVERT: J 680 GLN cc_start: 0.8198 (mt0) cc_final: 0.7957 (pm20) REVERT: J 691 LEU cc_start: 0.8190 (mt) cc_final: 0.7721 (mm) REVERT: J 693 ASN cc_start: 0.8324 (t0) cc_final: 0.8095 (m-40) REVERT: J 757 MET cc_start: 0.9209 (ttt) cc_final: 0.8961 (tmm) REVERT: K 167 TRP cc_start: 0.7581 (p90) cc_final: 0.7309 (p90) REVERT: K 231 LYS cc_start: 0.4976 (tttt) cc_final: 0.4713 (tttt) REVERT: K 297 TRP cc_start: 0.7590 (m100) cc_final: 0.7161 (m100) REVERT: K 365 TYR cc_start: 0.8057 (p90) cc_final: 0.7848 (p90) REVERT: K 423 LEU cc_start: 0.8518 (tp) cc_final: 0.7979 (pp) REVERT: K 465 LEU cc_start: 0.9678 (mt) cc_final: 0.9367 (mt) REVERT: K 566 ARG cc_start: 0.7885 (ttt-90) cc_final: 0.7262 (tmt170) REVERT: K 644 GLU cc_start: 0.8670 (tt0) cc_final: 0.8269 (tt0) REVERT: L 375 LEU cc_start: 0.9552 (mt) cc_final: 0.9181 (mt) REVERT: L 383 GLN cc_start: 0.8662 (mm110) cc_final: 0.8403 (mp10) REVERT: L 506 ASP cc_start: 0.6939 (p0) cc_final: 0.6706 (p0) REVERT: L 637 MET cc_start: 0.7770 (ppp) cc_final: 0.7414 (ppp) REVERT: M 53 ASP cc_start: 0.8650 (p0) cc_final: 0.7864 (p0) REVERT: M 73 ARG cc_start: 0.4848 (mtt-85) cc_final: 0.4330 (mmt180) REVERT: O 157 LEU cc_start: 0.9217 (pp) cc_final: 0.8885 (pp) REVERT: Q 102 ASN cc_start: 0.9432 (m110) cc_final: 0.9165 (t0) REVERT: Q 104 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8456 (tm-30) REVERT: Q 111 GLU cc_start: 0.9053 (tp30) cc_final: 0.8738 (tm-30) REVERT: R 75 ARG cc_start: 0.8473 (ttt90) cc_final: 0.8270 (mtt180) REVERT: R 282 MET cc_start: 0.9045 (tpp) cc_final: 0.8787 (tpp) REVERT: R 428 ILE cc_start: 0.9744 (pt) cc_final: 0.9512 (pt) REVERT: R 574 MET cc_start: 0.2090 (mmt) cc_final: 0.1734 (mmm) REVERT: R 831 VAL cc_start: 0.9320 (t) cc_final: 0.9016 (m) REVERT: R 853 MET cc_start: 0.8534 (ppp) cc_final: 0.7984 (ppp) REVERT: R 922 MET cc_start: 0.9653 (mtt) cc_final: 0.9406 (mtt) REVERT: R 988 LEU cc_start: 0.9168 (pt) cc_final: 0.8949 (pt) REVERT: R 995 TYR cc_start: 0.8936 (m-10) cc_final: 0.8621 (m-10) REVERT: R 1268 ILE cc_start: 0.9319 (mp) cc_final: 0.9117 (mp) REVERT: R 1277 MET cc_start: 0.9563 (mmm) cc_final: 0.9064 (mmp) REVERT: R 1290 TYR cc_start: 0.8724 (m-10) cc_final: 0.8285 (m-10) REVERT: R 1291 MET cc_start: 0.7701 (ttt) cc_final: 0.7126 (pmm) REVERT: R 1304 MET cc_start: 0.8417 (mmm) cc_final: 0.7973 (mmm) REVERT: R 1327 LEU cc_start: 0.8679 (tp) cc_final: 0.8289 (pp) REVERT: S 72 MET cc_start: 0.8637 (mtt) cc_final: 0.8320 (mtm) REVERT: S 264 VAL cc_start: 0.9283 (t) cc_final: 0.8932 (t) REVERT: S 268 MET cc_start: 0.8219 (mtt) cc_final: 0.7548 (mtp) REVERT: S 678 GLN cc_start: 0.8273 (tp40) cc_final: 0.7824 (tm-30) REVERT: S 938 ARG cc_start: 0.6609 (pmt-80) cc_final: 0.5096 (tmt-80) REVERT: V 18 ILE cc_start: 0.9638 (mm) cc_final: 0.9337 (mm) REVERT: V 245 HIS cc_start: 0.9388 (m-70) cc_final: 0.9115 (m-70) REVERT: X 79 GLN cc_start: 0.9168 (mm110) cc_final: 0.8936 (mm110) REVERT: X 119 LEU cc_start: 0.9425 (tp) cc_final: 0.9034 (tp) REVERT: Y 51 ILE cc_start: 0.9175 (tp) cc_final: 0.8856 (mm) REVERT: Y 91 LYS cc_start: 0.9457 (tttt) cc_final: 0.9235 (tttp) outliers start: 0 outliers final: 0 residues processed: 841 average time/residue: 0.4696 time to fit residues: 677.6566 Evaluate side-chains 608 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 608 time to evaluate : 4.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 651 optimal weight: 4.9990 chunk 585 optimal weight: 0.6980 chunk 324 optimal weight: 0.0670 chunk 199 optimal weight: 0.0020 chunk 394 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 605 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 367 optimal weight: 20.0000 chunk 450 optimal weight: 0.0010 chunk 701 optimal weight: 0.0770 overall best weight: 0.1690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 799 HIS I 834 HIS ** I 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 919 HIS J 629 ASN J 637 HIS J 763 GLN K 48 HIS ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 HIS K 270 HIS K 535 HIS ** K 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 HIS M 134 HIS Q 102 ASN R 378 GLN R 534 HIS R 552 HIS R 628 HIS R 726 ASN R 730 HIS R 907 ASN ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R1059 ASN R1320 ASN S 157 GLN S 370 GLN S 678 GLN S 758 HIS S 764 GLN V 252 HIS W 79 GLN W 90 GLN W 97 GLN ** W 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 166 GLN Y 57 ASN Y 81 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 50316 Z= 0.173 Angle : 0.622 10.873 69242 Z= 0.317 Chirality : 0.042 0.214 8528 Planarity : 0.004 0.074 9242 Dihedral : 4.242 38.590 8063 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.64 % Favored : 89.32 % Rotamer: Outliers : 0.17 % Allowed : 4.83 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.57 (0.10), residues: 7647 helix: 0.78 (0.09), residues: 3572 sheet: -3.54 (0.21), residues: 387 loop : -4.33 (0.09), residues: 3688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 806 HIS 0.010 0.001 HIS S 758 PHE 0.034 0.001 PHE S 340 TYR 0.016 0.001 TYR V 236 ARG 0.009 0.000 ARG L 505 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 768 time to evaluate : 4.270 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 TYR cc_start: 0.7287 (t80) cc_final: 0.6260 (m-10) REVERT: I 299 TYR cc_start: 0.8790 (m-80) cc_final: 0.8271 (m-80) REVERT: I 312 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8443 (mm-30) REVERT: I 409 ASP cc_start: 0.8627 (t0) cc_final: 0.8422 (t0) REVERT: I 503 LYS cc_start: 0.9385 (pttp) cc_final: 0.9092 (pttm) REVERT: I 512 LYS cc_start: 0.9490 (ttmt) cc_final: 0.9201 (mtpp) REVERT: I 577 MET cc_start: 0.8583 (ppp) cc_final: 0.8312 (ppp) REVERT: I 718 LEU cc_start: 0.8426 (pp) cc_final: 0.7692 (tp) REVERT: I 729 GLU cc_start: 0.7234 (tt0) cc_final: 0.6193 (tt0) REVERT: I 896 MET cc_start: 0.8691 (pmm) cc_final: 0.8340 (pmm) REVERT: I 920 ILE cc_start: 0.9389 (pt) cc_final: 0.8995 (mm) REVERT: I 922 LEU cc_start: 0.8586 (tp) cc_final: 0.8339 (tp) REVERT: I 1209 CYS cc_start: 0.7463 (t) cc_final: 0.6388 (t) REVERT: I 1214 ARG cc_start: 0.9164 (ptt-90) cc_final: 0.8947 (ptp90) REVERT: J 647 MET cc_start: 0.8844 (tpp) cc_final: 0.8474 (tpp) REVERT: J 670 ASP cc_start: 0.8336 (t0) cc_final: 0.8062 (t0) REVERT: J 693 ASN cc_start: 0.8311 (t0) cc_final: 0.8059 (m-40) REVERT: J 757 MET cc_start: 0.9313 (ttt) cc_final: 0.9021 (tmm) REVERT: K 23 LEU cc_start: 0.9020 (mt) cc_final: 0.8794 (mt) REVERT: K 167 TRP cc_start: 0.7446 (p90) cc_final: 0.7139 (p90) REVERT: K 231 LYS cc_start: 0.4850 (tttt) cc_final: 0.4560 (tttt) REVERT: K 297 TRP cc_start: 0.7833 (m100) cc_final: 0.7342 (m100) REVERT: K 365 TYR cc_start: 0.7992 (p90) cc_final: 0.7734 (p90) REVERT: K 423 LEU cc_start: 0.8536 (tp) cc_final: 0.8155 (pp) REVERT: K 465 LEU cc_start: 0.9689 (mt) cc_final: 0.9425 (mt) REVERT: K 540 LEU cc_start: 0.9152 (mt) cc_final: 0.8899 (pp) REVERT: K 566 ARG cc_start: 0.7762 (ttt-90) cc_final: 0.7211 (tmt170) REVERT: K 644 GLU cc_start: 0.8693 (tt0) cc_final: 0.8420 (tt0) REVERT: K 680 LEU cc_start: 0.9796 (pp) cc_final: 0.9485 (pp) REVERT: L 375 LEU cc_start: 0.9621 (mt) cc_final: 0.9354 (mt) REVERT: L 383 GLN cc_start: 0.8810 (mm110) cc_final: 0.8408 (mp10) REVERT: L 506 ASP cc_start: 0.6916 (p0) cc_final: 0.6646 (p0) REVERT: L 637 MET cc_start: 0.7437 (ppp) cc_final: 0.7133 (ppp) REVERT: M 32 LEU cc_start: 0.8869 (mt) cc_final: 0.8622 (mt) REVERT: M 136 PHE cc_start: 0.8921 (m-80) cc_final: 0.8673 (m-80) REVERT: Q 111 GLU cc_start: 0.8832 (tp30) cc_final: 0.8409 (tm-30) REVERT: R 44 PHE cc_start: 0.8641 (t80) cc_final: 0.8193 (t80) REVERT: R 75 ARG cc_start: 0.8317 (ttt90) cc_final: 0.8093 (mtt180) REVERT: R 525 MET cc_start: 0.6998 (mmp) cc_final: 0.6705 (mmp) REVERT: R 598 TRP cc_start: 0.7529 (t60) cc_final: 0.7312 (t60) REVERT: R 679 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8384 (mp0) REVERT: R 853 MET cc_start: 0.8426 (ppp) cc_final: 0.7922 (ppp) REVERT: R 871 MET cc_start: 0.9108 (tpt) cc_final: 0.8889 (tpt) REVERT: R 922 MET cc_start: 0.9633 (mtt) cc_final: 0.9413 (mtp) REVERT: R 994 LEU cc_start: 0.9391 (tp) cc_final: 0.9141 (tp) REVERT: R 1113 MET cc_start: 0.5326 (ptt) cc_final: 0.5034 (ptt) REVERT: R 1128 ASN cc_start: 0.8778 (m110) cc_final: 0.8466 (m110) REVERT: R 1146 MET cc_start: 0.9619 (mtp) cc_final: 0.9235 (mtp) REVERT: R 1224 LEU cc_start: 0.9523 (mm) cc_final: 0.9180 (mt) REVERT: R 1233 GLU cc_start: 0.8907 (pm20) cc_final: 0.8671 (mp0) REVERT: R 1247 TYR cc_start: 0.9416 (t80) cc_final: 0.9001 (t80) REVERT: R 1277 MET cc_start: 0.9524 (mmm) cc_final: 0.9028 (mmp) REVERT: R 1290 TYR cc_start: 0.8716 (m-80) cc_final: 0.8270 (m-10) REVERT: R 1291 MET cc_start: 0.7883 (ttt) cc_final: 0.7188 (pmm) REVERT: R 1304 MET cc_start: 0.8499 (mmm) cc_final: 0.7997 (mmm) REVERT: R 1327 LEU cc_start: 0.8704 (tp) cc_final: 0.8359 (pp) REVERT: S 72 MET cc_start: 0.8798 (mtt) cc_final: 0.8245 (mtm) REVERT: S 166 GLU cc_start: 0.8077 (tt0) cc_final: 0.7679 (pt0) REVERT: S 264 VAL cc_start: 0.9178 (t) cc_final: 0.8821 (t) REVERT: S 268 MET cc_start: 0.8205 (mtt) cc_final: 0.7750 (mtp) REVERT: S 671 MET cc_start: 0.9350 (tmm) cc_final: 0.9128 (tmm) REVERT: S 763 VAL cc_start: 0.9592 (p) cc_final: 0.9320 (m) REVERT: S 810 LEU cc_start: 0.9276 (mt) cc_final: 0.8973 (mt) REVERT: S 938 ARG cc_start: 0.6474 (pmt-80) cc_final: 0.5020 (tmt-80) REVERT: T 146 CYS cc_start: 0.8715 (t) cc_final: 0.8265 (t) REVERT: V 245 HIS cc_start: 0.9398 (m-70) cc_final: 0.9120 (m-70) REVERT: X 119 LEU cc_start: 0.9394 (tp) cc_final: 0.9019 (tp) REVERT: Y 84 GLN cc_start: 0.9368 (tt0) cc_final: 0.8903 (tt0) REVERT: Y 91 LYS cc_start: 0.9435 (tttt) cc_final: 0.8940 (tptt) REVERT: Y 173 MET cc_start: 0.6267 (mtp) cc_final: 0.5992 (mtp) outliers start: 5 outliers final: 2 residues processed: 770 average time/residue: 0.4511 time to fit residues: 605.7867 Evaluate side-chains 593 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 591 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 389 optimal weight: 7.9990 chunk 217 optimal weight: 0.0670 chunk 583 optimal weight: 10.0000 chunk 477 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 702 optimal weight: 4.9990 chunk 758 optimal weight: 0.0070 chunk 625 optimal weight: 9.9990 chunk 696 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 563 optimal weight: 4.9990 overall best weight: 2.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 866 ASN ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 637 HIS K 270 HIS ** K 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 216 HIS ** L 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 372 ASN ** L 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 461 HIS L 464 ASN ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 HIS ** Q 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 622 GLN R 664 GLN R 725 HIS R 747 ASN ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R1010 HIS R1165 HIS S 129 HIS S 157 GLN T 209 GLN V 120 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 50316 Z= 0.268 Angle : 0.665 10.406 69242 Z= 0.351 Chirality : 0.042 0.255 8528 Planarity : 0.005 0.090 9242 Dihedral : 4.629 35.695 8063 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.58 % Favored : 87.39 % Rotamer: Outliers : 0.20 % Allowed : 6.47 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.25 % 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: -2.20 (0.10), residues: 7647 helix: 1.11 (0.09), residues: 3573 sheet: -3.40 (0.22), residues: 413 loop : -4.16 (0.09), residues: 3661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 425 HIS 0.012 0.002 HIS R 925 PHE 0.033 0.002 PHE Y 52 TYR 0.027 0.002 TYR R1186 ARG 0.011 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 714 time to evaluate : 4.301 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: 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: H 99 TYR cc_start: 0.7764 (t80) cc_final: 0.7012 (m-10) REVERT: I 312 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8471 (mm-30) REVERT: I 503 LYS cc_start: 0.9437 (pttp) cc_final: 0.9166 (pttm) REVERT: I 577 MET cc_start: 0.8944 (ppp) cc_final: 0.8528 (ppp) REVERT: I 660 PHE cc_start: 0.8579 (m-80) cc_final: 0.8320 (m-10) REVERT: I 729 GLU cc_start: 0.7431 (tt0) cc_final: 0.6993 (tt0) REVERT: I 890 LYS cc_start: 0.9159 (mptt) cc_final: 0.8686 (mptt) REVERT: I 896 MET cc_start: 0.8796 (pmm) cc_final: 0.8481 (pmm) REVERT: I 920 ILE cc_start: 0.9513 (pt) cc_final: 0.9131 (mm) REVERT: I 1214 ARG cc_start: 0.9238 (ptt-90) cc_final: 0.8844 (ptt180) REVERT: J 647 MET cc_start: 0.8847 (tpp) cc_final: 0.8529 (tpp) REVERT: J 670 ASP cc_start: 0.8337 (t0) cc_final: 0.7976 (t0) REVERT: J 693 ASN cc_start: 0.8433 (t0) cc_final: 0.8224 (m-40) REVERT: J 757 MET cc_start: 0.9449 (ttt) cc_final: 0.9169 (tmm) REVERT: K 214 ILE cc_start: 0.8885 (mp) cc_final: 0.8599 (mm) REVERT: K 423 LEU cc_start: 0.8617 (tp) cc_final: 0.8107 (pp) REVERT: K 465 LEU cc_start: 0.9725 (mt) cc_final: 0.9396 (mt) REVERT: K 566 ARG cc_start: 0.7652 (ttt-90) cc_final: 0.7110 (tmt170) REVERT: K 608 VAL cc_start: 0.9330 (m) cc_final: 0.9121 (p) REVERT: L 383 GLN cc_start: 0.8852 (mm110) cc_final: 0.8476 (mp10) REVERT: M 32 LEU cc_start: 0.8956 (mt) cc_final: 0.8647 (mt) REVERT: M 33 GLU cc_start: 0.8858 (pp20) cc_final: 0.8526 (pp20) REVERT: R 75 ARG cc_start: 0.8588 (ttt90) cc_final: 0.8139 (ptm160) REVERT: R 85 MET cc_start: 0.8639 (mmm) cc_final: 0.8387 (mmp) REVERT: R 210 ASP cc_start: 0.8027 (m-30) cc_final: 0.7630 (m-30) REVERT: R 286 MET cc_start: 0.9735 (tmm) cc_final: 0.9386 (tmm) REVERT: R 598 TRP cc_start: 0.7491 (t60) cc_final: 0.7250 (t60) REVERT: R 853 MET cc_start: 0.8538 (ppp) cc_final: 0.7995 (ppp) REVERT: R 871 MET cc_start: 0.9166 (tpt) cc_final: 0.8960 (tpt) REVERT: R 994 LEU cc_start: 0.9228 (tp) cc_final: 0.9018 (tp) REVERT: R 1128 ASN cc_start: 0.8897 (m110) cc_final: 0.8610 (m110) REVERT: R 1146 MET cc_start: 0.9659 (mtp) cc_final: 0.9427 (mtp) REVERT: R 1197 HIS cc_start: 0.8497 (t-170) cc_final: 0.8081 (t70) REVERT: R 1277 MET cc_start: 0.9551 (mmm) cc_final: 0.9033 (mmm) REVERT: R 1290 TYR cc_start: 0.8928 (m-80) cc_final: 0.8722 (m-10) REVERT: R 1304 MET cc_start: 0.8414 (mmm) cc_final: 0.7996 (mmm) REVERT: R 1327 LEU cc_start: 0.8941 (tp) cc_final: 0.8554 (pp) REVERT: S 72 MET cc_start: 0.8961 (mtt) cc_final: 0.8625 (mtt) REVERT: S 125 LEU cc_start: 0.9744 (tp) cc_final: 0.9544 (tp) REVERT: S 285 ILE cc_start: 0.9588 (tp) cc_final: 0.9374 (tp) REVERT: S 671 MET cc_start: 0.9367 (tmm) cc_final: 0.9127 (tmm) REVERT: T 46 TYR cc_start: 0.9071 (t80) cc_final: 0.8867 (t80) REVERT: T 128 PHE cc_start: 0.9415 (m-80) cc_final: 0.9158 (m-80) REVERT: T 146 CYS cc_start: 0.8781 (t) cc_final: 0.8351 (t) REVERT: V 245 HIS cc_start: 0.9503 (m-70) cc_final: 0.9194 (m-70) REVERT: W 64 TYR cc_start: 0.8762 (t80) cc_final: 0.8257 (t80) REVERT: X 119 LEU cc_start: 0.9585 (tp) cc_final: 0.9241 (tp) REVERT: Y 84 GLN cc_start: 0.9387 (tt0) cc_final: 0.8908 (mt0) outliers start: 6 outliers final: 3 residues processed: 719 average time/residue: 0.5118 time to fit residues: 653.3022 Evaluate side-chains 551 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 548 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 693 optimal weight: 0.0870 chunk 528 optimal weight: 10.0000 chunk 364 optimal weight: 0.7980 chunk 77 optimal weight: 0.0570 chunk 335 optimal weight: 0.2980 chunk 471 optimal weight: 1.9990 chunk 704 optimal weight: 0.8980 chunk 746 optimal weight: 2.9990 chunk 368 optimal weight: 0.4980 chunk 668 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 637 HIS ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 HIS L 381 HIS ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 ASN R 684 ASN R 918 HIS R1028 HIS ** S 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 166 GLN Y 23 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 50316 Z= 0.164 Angle : 0.618 12.579 69242 Z= 0.311 Chirality : 0.042 0.455 8528 Planarity : 0.004 0.088 9242 Dihedral : 4.391 38.531 8063 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.80 % Favored : 89.16 % Rotamer: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.25 % Twisted General : 0.01 % 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: -1.82 (0.10), residues: 7647 helix: 1.45 (0.09), residues: 3585 sheet: -3.08 (0.23), residues: 396 loop : -4.02 (0.09), residues: 3666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP K 167 HIS 0.021 0.001 HIS J 706 PHE 0.022 0.001 PHE R1191 TYR 0.035 0.001 TYR V 111 ARG 0.009 0.000 ARG R1328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 724 time to evaluate : 4.303 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 ARG cc_start: 0.9278 (mpp-170) cc_final: 0.8897 (mtt90) REVERT: H 99 TYR cc_start: 0.7401 (t80) cc_final: 0.6761 (m-10) REVERT: I 312 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8473 (mm-30) REVERT: I 320 MET cc_start: 0.9073 (tpt) cc_final: 0.8785 (tpp) REVERT: I 460 ILE cc_start: 0.8664 (tt) cc_final: 0.8394 (mp) REVERT: I 503 LYS cc_start: 0.9392 (pttp) cc_final: 0.9123 (pttm) REVERT: I 577 MET cc_start: 0.8842 (ppp) cc_final: 0.8485 (ppp) REVERT: I 653 MET cc_start: 0.9194 (mmt) cc_final: 0.8980 (mtt) REVERT: I 718 LEU cc_start: 0.8734 (pp) cc_final: 0.8012 (tp) REVERT: I 890 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8811 (mptt) REVERT: I 896 MET cc_start: 0.8780 (pmm) cc_final: 0.8450 (pmm) REVERT: I 1209 CYS cc_start: 0.7620 (t) cc_final: 0.6639 (t) REVERT: J 647 MET cc_start: 0.8870 (tpp) cc_final: 0.8402 (tpp) REVERT: J 670 ASP cc_start: 0.8327 (t0) cc_final: 0.8010 (t0) REVERT: J 693 ASN cc_start: 0.8446 (t0) cc_final: 0.8056 (m-40) REVERT: J 757 MET cc_start: 0.9450 (ttt) cc_final: 0.9167 (tmm) REVERT: K 297 TRP cc_start: 0.8202 (m100) cc_final: 0.7734 (m100) REVERT: K 423 LEU cc_start: 0.8750 (tp) cc_final: 0.8278 (pp) REVERT: K 465 LEU cc_start: 0.9702 (mt) cc_final: 0.9417 (mt) REVERT: K 540 LEU cc_start: 0.9266 (mt) cc_final: 0.8950 (pp) REVERT: K 566 ARG cc_start: 0.7491 (ttt-90) cc_final: 0.7024 (tmt170) REVERT: K 608 VAL cc_start: 0.9200 (m) cc_final: 0.8943 (p) REVERT: K 644 GLU cc_start: 0.8834 (tt0) cc_final: 0.8570 (tt0) REVERT: L 327 ASN cc_start: 0.7853 (t0) cc_final: 0.7352 (t0) REVERT: L 375 LEU cc_start: 0.9594 (mt) cc_final: 0.9354 (mt) REVERT: L 383 GLN cc_start: 0.8808 (mm110) cc_final: 0.8431 (mp10) REVERT: L 637 MET cc_start: 0.7441 (ppp) cc_final: 0.7218 (ppp) REVERT: M 32 LEU cc_start: 0.8929 (mt) cc_final: 0.8406 (mt) REVERT: O 119 TYR cc_start: 0.8929 (t80) cc_final: 0.8642 (t80) REVERT: R 44 PHE cc_start: 0.8530 (t80) cc_final: 0.8126 (t80) REVERT: R 75 ARG cc_start: 0.8396 (ttt90) cc_final: 0.8121 (mtt180) REVERT: R 85 MET cc_start: 0.8533 (mmm) cc_final: 0.8327 (mmp) REVERT: R 282 MET cc_start: 0.9478 (tmm) cc_final: 0.9145 (tmm) REVERT: R 286 MET cc_start: 0.9718 (tmm) cc_final: 0.9364 (tmm) REVERT: R 525 MET cc_start: 0.7437 (mmp) cc_final: 0.6598 (mmt) REVERT: R 598 TRP cc_start: 0.7369 (t60) cc_final: 0.7063 (t60) REVERT: R 853 MET cc_start: 0.8549 (ppp) cc_final: 0.7981 (ppp) REVERT: R 1113 MET cc_start: 0.5508 (ptt) cc_final: 0.5117 (ptt) REVERT: R 1128 ASN cc_start: 0.8872 (m110) cc_final: 0.8547 (m110) REVERT: R 1146 MET cc_start: 0.9592 (mtp) cc_final: 0.9130 (ptp) REVERT: R 1197 HIS cc_start: 0.8492 (t-170) cc_final: 0.8052 (t-90) REVERT: R 1277 MET cc_start: 0.9525 (mmm) cc_final: 0.9018 (mmp) REVERT: R 1290 TYR cc_start: 0.8752 (m-80) cc_final: 0.8256 (m-10) REVERT: R 1291 MET cc_start: 0.8311 (ttm) cc_final: 0.7632 (pmm) REVERT: R 1304 MET cc_start: 0.8473 (mmm) cc_final: 0.8029 (mmm) REVERT: R 1327 LEU cc_start: 0.8852 (tp) cc_final: 0.8448 (pp) REVERT: S 72 MET cc_start: 0.8813 (mtt) cc_final: 0.8353 (mtm) REVERT: S 228 MET cc_start: 0.7844 (tpt) cc_final: 0.7628 (tpp) REVERT: S 268 MET cc_start: 0.8055 (mtt) cc_final: 0.7375 (mtp) REVERT: S 285 ILE cc_start: 0.9591 (tp) cc_final: 0.9345 (tp) REVERT: S 671 MET cc_start: 0.9382 (tmm) cc_final: 0.9061 (tmm) REVERT: S 763 VAL cc_start: 0.9588 (p) cc_final: 0.9314 (m) REVERT: T 128 PHE cc_start: 0.9375 (m-80) cc_final: 0.9118 (m-80) REVERT: T 146 CYS cc_start: 0.8824 (t) cc_final: 0.8427 (t) REVERT: V 245 HIS cc_start: 0.9450 (m-70) cc_final: 0.9116 (m-70) REVERT: W 96 LEU cc_start: 0.9030 (mt) cc_final: 0.8765 (mt) REVERT: X 119 LEU cc_start: 0.9271 (tp) cc_final: 0.9068 (tp) REVERT: Y 84 GLN cc_start: 0.9372 (tt0) cc_final: 0.8858 (tt0) outliers start: 1 outliers final: 0 residues processed: 725 average time/residue: 0.4358 time to fit residues: 553.6150 Evaluate side-chains 563 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 4.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 621 optimal weight: 0.8980 chunk 423 optimal weight: 20.0000 chunk 10 optimal weight: 0.0070 chunk 555 optimal weight: 0.8980 chunk 307 optimal weight: 0.0070 chunk 636 optimal weight: 0.0980 chunk 515 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 381 optimal weight: 0.8980 chunk 669 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 GLN ** I 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 859 HIS J 637 HIS ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 622 GLN ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 998 HIS ** W 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 50316 Z= 0.158 Angle : 0.605 12.519 69242 Z= 0.304 Chirality : 0.041 0.353 8528 Planarity : 0.004 0.079 9242 Dihedral : 4.262 36.546 8063 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.96 % Favored : 89.03 % Rotamer: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.00 % 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: -1.65 (0.10), residues: 7647 helix: 1.60 (0.09), residues: 3586 sheet: -2.89 (0.24), residues: 397 loop : -3.96 (0.09), residues: 3664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 721 HIS 0.021 0.001 HIS J 706 PHE 0.023 0.001 PHE R 584 TYR 0.016 0.001 TYR K 365 ARG 0.007 0.000 ARG R1328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 735 time to evaluate : 4.218 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 TYR cc_start: 0.7537 (t80) cc_final: 0.6690 (m-10) REVERT: I 312 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8489 (mm-30) REVERT: I 320 MET cc_start: 0.9055 (tpt) cc_final: 0.8763 (tpp) REVERT: I 460 ILE cc_start: 0.8435 (tt) cc_final: 0.8089 (mp) REVERT: I 503 LYS cc_start: 0.9431 (pttp) cc_final: 0.9171 (pttm) REVERT: I 577 MET cc_start: 0.8866 (ppp) cc_final: 0.8519 (ppp) REVERT: I 718 LEU cc_start: 0.8865 (pp) cc_final: 0.7992 (tp) REVERT: I 896 MET cc_start: 0.8740 (pmm) cc_final: 0.8448 (pmm) REVERT: I 920 ILE cc_start: 0.9414 (pt) cc_final: 0.8984 (mm) REVERT: I 1209 CYS cc_start: 0.7300 (t) cc_final: 0.6876 (t) REVERT: J 647 MET cc_start: 0.8896 (tpp) cc_final: 0.8460 (tpp) REVERT: J 670 ASP cc_start: 0.8265 (t0) cc_final: 0.7875 (t0) REVERT: J 693 ASN cc_start: 0.8368 (t0) cc_final: 0.8014 (m-40) REVERT: J 757 MET cc_start: 0.9469 (ttt) cc_final: 0.9156 (tmm) REVERT: K 423 LEU cc_start: 0.8769 (tp) cc_final: 0.8233 (pt) REVERT: K 465 LEU cc_start: 0.9702 (mt) cc_final: 0.9411 (mt) REVERT: K 540 LEU cc_start: 0.9239 (mt) cc_final: 0.8923 (pp) REVERT: K 566 ARG cc_start: 0.7776 (tmt170) cc_final: 0.7089 (tmt170) REVERT: K 608 VAL cc_start: 0.9244 (m) cc_final: 0.8982 (p) REVERT: L 327 ASN cc_start: 0.7787 (t0) cc_final: 0.7396 (t0) REVERT: L 375 LEU cc_start: 0.9586 (mt) cc_final: 0.9302 (mt) REVERT: L 383 GLN cc_start: 0.8855 (mm110) cc_final: 0.8459 (mp10) REVERT: M 32 LEU cc_start: 0.8820 (mt) cc_final: 0.8509 (mt) REVERT: O 119 TYR cc_start: 0.8890 (t80) cc_final: 0.8633 (t80) REVERT: R 44 PHE cc_start: 0.8550 (t80) cc_final: 0.8139 (t80) REVERT: R 75 ARG cc_start: 0.8345 (ttt90) cc_final: 0.8084 (mtt90) REVERT: R 85 MET cc_start: 0.8496 (mmm) cc_final: 0.8293 (mmp) REVERT: R 282 MET cc_start: 0.9473 (tmm) cc_final: 0.9123 (tmm) REVERT: R 286 MET cc_start: 0.9723 (tmm) cc_final: 0.9359 (tmm) REVERT: R 525 MET cc_start: 0.7406 (mmp) cc_final: 0.6561 (mmt) REVERT: R 598 TRP cc_start: 0.7362 (t60) cc_final: 0.7029 (t60) REVERT: R 853 MET cc_start: 0.8560 (ppp) cc_final: 0.8011 (ppp) REVERT: R 871 MET cc_start: 0.9313 (tpt) cc_final: 0.8750 (tpp) REVERT: R 988 LEU cc_start: 0.9519 (pt) cc_final: 0.9311 (pt) REVERT: R 1113 MET cc_start: 0.5364 (ptt) cc_final: 0.5010 (ptt) REVERT: R 1128 ASN cc_start: 0.8885 (m110) cc_final: 0.8554 (m110) REVERT: R 1146 MET cc_start: 0.9583 (mtp) cc_final: 0.9110 (ptp) REVERT: R 1197 HIS cc_start: 0.8526 (t-170) cc_final: 0.8279 (t70) REVERT: R 1277 MET cc_start: 0.9519 (mmm) cc_final: 0.9016 (mmp) REVERT: R 1290 TYR cc_start: 0.8737 (m-80) cc_final: 0.8295 (m-10) REVERT: R 1291 MET cc_start: 0.8235 (ttm) cc_final: 0.7629 (pmm) REVERT: R 1304 MET cc_start: 0.8435 (mmm) cc_final: 0.7981 (mmm) REVERT: R 1327 LEU cc_start: 0.8815 (tp) cc_final: 0.8432 (pp) REVERT: S 72 MET cc_start: 0.8690 (mtt) cc_final: 0.8267 (mtm) REVERT: S 285 ILE cc_start: 0.9586 (tp) cc_final: 0.9332 (tp) REVERT: S 671 MET cc_start: 0.9356 (tmm) cc_final: 0.9081 (tmm) REVERT: S 833 ARG cc_start: 0.8073 (tmt-80) cc_final: 0.7677 (tpm170) REVERT: T 128 PHE cc_start: 0.9358 (m-80) cc_final: 0.9021 (m-80) REVERT: T 146 CYS cc_start: 0.8860 (t) cc_final: 0.8409 (t) REVERT: V 22 GLN cc_start: 0.8807 (tt0) cc_final: 0.8587 (tt0) REVERT: V 245 HIS cc_start: 0.9455 (m-70) cc_final: 0.9153 (m-70) REVERT: W 85 LEU cc_start: 0.9197 (mp) cc_final: 0.8708 (tp) REVERT: W 90 GLN cc_start: 0.9037 (mp10) cc_final: 0.8660 (mp10) REVERT: X 119 LEU cc_start: 0.9356 (tp) cc_final: 0.9093 (tp) REVERT: Y 84 GLN cc_start: 0.9369 (tt0) cc_final: 0.8878 (tt0) outliers start: 3 outliers final: 0 residues processed: 738 average time/residue: 0.4616 time to fit residues: 602.1547 Evaluate side-chains 577 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 4.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 251 optimal weight: 10.0000 chunk 672 optimal weight: 10.0000 chunk 147 optimal weight: 50.0000 chunk 438 optimal weight: 50.0000 chunk 184 optimal weight: 0.0170 chunk 746 optimal weight: 0.8980 chunk 620 optimal weight: 0.8980 chunk 345 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 247 optimal weight: 8.9990 chunk 392 optimal weight: 9.9990 overall best weight: 4.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN K 483 GLN L 332 GLN ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN M 54 HIS Q 84 GLN R 332 GLN R 333 HIS ** R 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 49 GLN ** S 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 697 ASN S 784 HIS S 834 HIS ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 50316 Z= 0.429 Angle : 0.850 18.182 69242 Z= 0.458 Chirality : 0.047 0.399 8528 Planarity : 0.006 0.105 9242 Dihedral : 5.561 36.636 8063 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 15.80 % Favored : 84.16 % Rotamer: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.25 % Twisted General : 0.05 % 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: -2.24 (0.10), residues: 7647 helix: 0.99 (0.09), residues: 3585 sheet: -3.38 (0.22), residues: 432 loop : -4.10 (0.09), residues: 3630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP R 48 HIS 0.021 0.003 HIS J 706 PHE 0.034 0.003 PHE K 208 TYR 0.049 0.004 TYR I 555 ARG 0.017 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 627 time to evaluate : 4.183 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: symmetry clash revert: symmetry clash REVERT: H 87 ARG cc_start: 0.8570 (mpp-170) cc_final: 0.8096 (mpp-170) REVERT: H 99 TYR cc_start: 0.8400 (t80) cc_final: 0.7692 (m-10) REVERT: I 312 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8632 (mm-30) REVERT: I 320 MET cc_start: 0.9165 (tpt) cc_final: 0.8962 (tpt) REVERT: I 503 LYS cc_start: 0.9468 (pttp) cc_final: 0.9256 (pttm) REVERT: I 653 MET cc_start: 0.9621 (mtm) cc_final: 0.9416 (mtt) REVERT: I 664 ARG cc_start: 0.9258 (tmm160) cc_final: 0.8967 (ttp80) REVERT: I 708 ASP cc_start: 0.9389 (m-30) cc_final: 0.9108 (m-30) REVERT: I 890 LYS cc_start: 0.9394 (mmtt) cc_final: 0.8884 (mmtp) REVERT: I 1221 MET cc_start: 0.8806 (mtt) cc_final: 0.8406 (ptt) REVERT: J 647 MET cc_start: 0.8895 (tpp) cc_final: 0.8513 (tpp) REVERT: J 670 ASP cc_start: 0.8445 (t0) cc_final: 0.8075 (t0) REVERT: K 23 LEU cc_start: 0.9112 (mp) cc_final: 0.8885 (mt) REVERT: K 75 LEU cc_start: 0.8476 (tt) cc_final: 0.8251 (tt) REVERT: K 423 LEU cc_start: 0.9052 (tp) cc_final: 0.8846 (tp) REVERT: K 465 LEU cc_start: 0.9716 (mt) cc_final: 0.9291 (mt) REVERT: K 566 ARG cc_start: 0.7990 (tmt170) cc_final: 0.7267 (tmt170) REVERT: L 375 LEU cc_start: 0.9502 (mt) cc_final: 0.9151 (mt) REVERT: L 383 GLN cc_start: 0.8886 (mm110) cc_final: 0.8550 (mp10) REVERT: L 637 MET cc_start: 0.7984 (ppp) cc_final: 0.7758 (ppp) REVERT: M 32 LEU cc_start: 0.9025 (mt) cc_final: 0.8661 (mt) REVERT: R 85 MET cc_start: 0.8825 (mmm) cc_final: 0.8523 (mmm) REVERT: R 210 ASP cc_start: 0.7867 (m-30) cc_final: 0.7643 (m-30) REVERT: R 286 MET cc_start: 0.9715 (tmm) cc_final: 0.9357 (tmm) REVERT: R 379 PHE cc_start: 0.9104 (t80) cc_final: 0.8848 (t80) REVERT: R 525 MET cc_start: 0.7522 (mmp) cc_final: 0.6606 (mmt) REVERT: R 598 TRP cc_start: 0.7567 (t60) cc_final: 0.7240 (t60) REVERT: R 607 MET cc_start: 0.7950 (mmt) cc_final: 0.7469 (mmm) REVERT: R 853 MET cc_start: 0.8677 (ppp) cc_final: 0.8210 (ppp) REVERT: R 871 MET cc_start: 0.9410 (tpt) cc_final: 0.9189 (tpp) REVERT: R 962 ARG cc_start: 0.8729 (ttt180) cc_final: 0.8225 (ttt180) REVERT: R 995 TYR cc_start: 0.8713 (m-80) cc_final: 0.8262 (m-80) REVERT: R 1128 ASN cc_start: 0.9193 (m110) cc_final: 0.8907 (m110) REVERT: R 1146 MET cc_start: 0.9641 (mtp) cc_final: 0.9372 (mtp) REVERT: R 1277 MET cc_start: 0.9606 (mmm) cc_final: 0.9100 (mmm) REVERT: R 1290 TYR cc_start: 0.9010 (m-80) cc_final: 0.8534 (m-10) REVERT: R 1291 MET cc_start: 0.8538 (ttm) cc_final: 0.7801 (pmm) REVERT: R 1304 MET cc_start: 0.8658 (mmm) cc_final: 0.8172 (mmm) REVERT: S 72 MET cc_start: 0.8678 (mtt) cc_final: 0.8211 (mtm) REVERT: S 766 LEU cc_start: 0.9640 (tp) cc_final: 0.9272 (tp) REVERT: V 245 HIS cc_start: 0.9512 (m-70) cc_final: 0.9240 (m-70) REVERT: W 64 TYR cc_start: 0.9122 (t80) cc_final: 0.8880 (t80) REVERT: W 90 GLN cc_start: 0.9351 (mp10) cc_final: 0.9056 (mp10) REVERT: W 96 LEU cc_start: 0.9071 (mt) cc_final: 0.8849 (mt) REVERT: X 79 GLN cc_start: 0.9325 (mm110) cc_final: 0.9053 (mm110) outliers start: 2 outliers final: 0 residues processed: 629 average time/residue: 0.4258 time to fit residues: 469.4193 Evaluate side-chains 497 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 4.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 720 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 425 optimal weight: 6.9990 chunk 545 optimal weight: 0.0970 chunk 422 optimal weight: 9.9990 chunk 628 optimal weight: 2.9990 chunk 417 optimal weight: 30.0000 chunk 744 optimal weight: 0.0470 chunk 465 optimal weight: 1.9990 chunk 453 optimal weight: 0.8980 chunk 343 optimal weight: 40.0000 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 686 HIS ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 270 HIS K 535 HIS L 461 HIS ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS R 333 HIS R 449 HIS ** R 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 370 GLN S 697 ASN T 38 HIS ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 50316 Z= 0.196 Angle : 0.667 13.091 69242 Z= 0.341 Chirality : 0.043 0.357 8528 Planarity : 0.005 0.096 9242 Dihedral : 4.990 37.926 8063 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.29 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.25 % Twisted General : 0.04 % 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: -1.78 (0.10), residues: 7647 helix: 1.45 (0.09), residues: 3598 sheet: -3.13 (0.22), residues: 446 loop : -3.97 (0.09), residues: 3603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 124 HIS 0.017 0.001 HIS J 706 PHE 0.038 0.002 PHE T 128 TYR 0.037 0.002 TYR V 111 ARG 0.008 0.001 ARG K 728 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 671 time to evaluate : 4.240 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 TYR cc_start: 0.8197 (t80) cc_final: 0.7211 (m-10) REVERT: I 312 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8567 (mm-30) REVERT: I 320 MET cc_start: 0.9105 (tpt) cc_final: 0.8841 (tpp) REVERT: I 460 ILE cc_start: 0.8823 (tt) cc_final: 0.8349 (mp) REVERT: I 577 MET cc_start: 0.9197 (ppp) cc_final: 0.8497 (ppp) REVERT: I 708 ASP cc_start: 0.9286 (m-30) cc_final: 0.9010 (m-30) REVERT: I 890 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8854 (mmtp) REVERT: J 647 MET cc_start: 0.8914 (tpp) cc_final: 0.8473 (tpp) REVERT: J 670 ASP cc_start: 0.8321 (t0) cc_final: 0.7913 (t0) REVERT: J 757 MET cc_start: 0.9527 (tmm) cc_final: 0.9223 (tmm) REVERT: K 75 LEU cc_start: 0.8182 (tt) cc_final: 0.7934 (tt) REVERT: K 423 LEU cc_start: 0.8848 (tp) cc_final: 0.8106 (pt) REVERT: K 465 LEU cc_start: 0.9713 (mt) cc_final: 0.9359 (mt) REVERT: K 566 ARG cc_start: 0.7894 (tmt170) cc_final: 0.7141 (tmt170) REVERT: K 642 LEU cc_start: 0.9690 (mt) cc_final: 0.9384 (tp) REVERT: K 644 GLU cc_start: 0.8840 (tt0) cc_final: 0.8621 (tt0) REVERT: K 649 ILE cc_start: 0.9773 (pt) cc_final: 0.9501 (pt) REVERT: L 375 LEU cc_start: 0.9571 (mt) cc_final: 0.9183 (mt) REVERT: L 378 ARG cc_start: 0.7409 (mmm160) cc_final: 0.7176 (mmm160) REVERT: L 383 GLN cc_start: 0.8817 (mm110) cc_final: 0.8458 (mp10) REVERT: L 637 MET cc_start: 0.7779 (ppp) cc_final: 0.7505 (ppp) REVERT: M 32 LEU cc_start: 0.8911 (mt) cc_final: 0.8511 (mt) REVERT: R 85 MET cc_start: 0.8632 (mmm) cc_final: 0.8391 (mmp) REVERT: R 286 MET cc_start: 0.9744 (tmm) cc_final: 0.9365 (tmm) REVERT: R 333 HIS cc_start: 0.9079 (m90) cc_final: 0.8680 (m-70) REVERT: R 525 MET cc_start: 0.7211 (mmp) cc_final: 0.6816 (mmp) REVERT: R 574 MET cc_start: 0.0765 (mmm) cc_final: 0.0382 (mmm) REVERT: R 598 TRP cc_start: 0.7434 (t60) cc_final: 0.7086 (t60) REVERT: R 607 MET cc_start: 0.7636 (mmt) cc_final: 0.7199 (mmt) REVERT: R 796 MET cc_start: 0.9035 (ptm) cc_final: 0.8775 (ppp) REVERT: R 853 MET cc_start: 0.8694 (ppp) cc_final: 0.8356 (ppp) REVERT: R 871 MET cc_start: 0.9269 (tpt) cc_final: 0.8977 (tpt) REVERT: R 995 TYR cc_start: 0.8707 (m-80) cc_final: 0.8238 (m-80) REVERT: R 1014 MET cc_start: 0.3649 (mmp) cc_final: 0.2686 (mpp) REVERT: R 1113 MET cc_start: 0.5479 (ptt) cc_final: 0.5144 (ptt) REVERT: R 1128 ASN cc_start: 0.9079 (m110) cc_final: 0.8772 (m110) REVERT: R 1146 MET cc_start: 0.9616 (mtp) cc_final: 0.9186 (ptp) REVERT: R 1277 MET cc_start: 0.9559 (mmm) cc_final: 0.9028 (mmm) REVERT: R 1290 TYR cc_start: 0.8854 (m-80) cc_final: 0.8379 (m-10) REVERT: R 1291 MET cc_start: 0.8316 (ttm) cc_final: 0.7585 (pmm) REVERT: R 1304 MET cc_start: 0.8608 (mmm) cc_final: 0.8235 (mmm) REVERT: R 1327 LEU cc_start: 0.8999 (tp) cc_final: 0.8586 (pp) REVERT: S 72 MET cc_start: 0.8460 (mtt) cc_final: 0.8143 (mtm) REVERT: S 729 ILE cc_start: 0.9547 (mt) cc_final: 0.9330 (mm) REVERT: S 760 LEU cc_start: 0.9485 (mm) cc_final: 0.9149 (tp) REVERT: V 22 GLN cc_start: 0.8945 (tt0) cc_final: 0.8654 (tt0) REVERT: V 111 TYR cc_start: 0.9057 (m-80) cc_final: 0.8765 (m-80) REVERT: V 245 HIS cc_start: 0.9465 (m-70) cc_final: 0.9146 (m-70) REVERT: W 90 GLN cc_start: 0.9205 (mp10) cc_final: 0.8924 (mp10) REVERT: W 97 GLN cc_start: 0.9216 (mm110) cc_final: 0.8690 (mm110) REVERT: X 79 GLN cc_start: 0.9279 (mm110) cc_final: 0.9003 (mm110) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.4281 time to fit residues: 505.3980 Evaluate side-chains 526 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 460 optimal weight: 10.0000 chunk 297 optimal weight: 0.0270 chunk 444 optimal weight: 50.0000 chunk 224 optimal weight: 0.1980 chunk 146 optimal weight: 60.0000 chunk 144 optimal weight: 50.0000 chunk 473 optimal weight: 0.9980 chunk 506 optimal weight: 0.9990 chunk 367 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 584 optimal weight: 2.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 686 HIS ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS L 365 HIS ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 332 GLN S 697 ASN ** W 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 50316 Z= 0.179 Angle : 0.649 12.842 69242 Z= 0.329 Chirality : 0.043 0.332 8528 Planarity : 0.005 0.088 9242 Dihedral : 4.706 37.278 8063 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.33 % Favored : 86.62 % Rotamer: Outliers : 0.03 % Allowed : 1.64 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.25 % 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: -1.59 (0.10), residues: 7647 helix: 1.67 (0.09), residues: 3607 sheet: -2.92 (0.23), residues: 429 loop : -3.97 (0.09), residues: 3611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP S 721 HIS 0.016 0.001 HIS J 706 PHE 0.026 0.001 PHE T 128 TYR 0.043 0.001 TYR R1068 ARG 0.006 0.000 ARG I 709 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 675 time to evaluate : 4.238 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: symmetry clash REVERT: H 92 MET cc_start: 0.8911 (ptp) cc_final: 0.8565 (ptp) REVERT: H 99 TYR cc_start: 0.8099 (t80) cc_final: 0.7403 (m-10) REVERT: I 312 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8509 (mm-30) REVERT: I 320 MET cc_start: 0.9112 (tpt) cc_final: 0.8844 (tpp) REVERT: I 460 ILE cc_start: 0.8884 (tt) cc_final: 0.8433 (mp) REVERT: I 653 MET cc_start: 0.9533 (mtm) cc_final: 0.8882 (mmm) REVERT: I 708 ASP cc_start: 0.9280 (m-30) cc_final: 0.8999 (m-30) REVERT: I 886 ASN cc_start: 0.9400 (t0) cc_final: 0.9138 (t0) REVERT: I 890 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8818 (mmtp) REVERT: J 647 MET cc_start: 0.8951 (tpp) cc_final: 0.8578 (tpp) REVERT: J 670 ASP cc_start: 0.8228 (t0) cc_final: 0.7852 (t0) REVERT: J 757 MET cc_start: 0.9565 (tmm) cc_final: 0.9240 (tmm) REVERT: K 75 LEU cc_start: 0.8086 (tt) cc_final: 0.7797 (tt) REVERT: K 423 LEU cc_start: 0.8757 (tp) cc_final: 0.8045 (pt) REVERT: K 465 LEU cc_start: 0.9715 (mt) cc_final: 0.9367 (mt) REVERT: K 566 ARG cc_start: 0.7764 (tmt170) cc_final: 0.7024 (tmt170) REVERT: K 644 GLU cc_start: 0.8914 (tt0) cc_final: 0.8666 (tt0) REVERT: L 327 ASN cc_start: 0.8168 (t0) cc_final: 0.7960 (t0) REVERT: L 375 LEU cc_start: 0.9564 (mt) cc_final: 0.9252 (mt) REVERT: L 378 ARG cc_start: 0.7472 (mmm160) cc_final: 0.7182 (mmm160) REVERT: L 383 GLN cc_start: 0.8814 (mm110) cc_final: 0.8420 (mp10) REVERT: L 629 GLU cc_start: 0.8464 (tp30) cc_final: 0.8163 (tp30) REVERT: M 32 LEU cc_start: 0.8979 (mt) cc_final: 0.8565 (mt) REVERT: R 85 MET cc_start: 0.8564 (mmm) cc_final: 0.8310 (mmp) REVERT: R 286 MET cc_start: 0.9703 (tmm) cc_final: 0.9337 (tmm) REVERT: R 333 HIS cc_start: 0.9077 (m90) cc_final: 0.8687 (m-70) REVERT: R 525 MET cc_start: 0.7287 (mmp) cc_final: 0.6819 (mmp) REVERT: R 796 MET cc_start: 0.9029 (ptm) cc_final: 0.8789 (ppp) REVERT: R 853 MET cc_start: 0.8657 (ppp) cc_final: 0.8303 (ppp) REVERT: R 871 MET cc_start: 0.9233 (tpt) cc_final: 0.8948 (tpt) REVERT: R 962 ARG cc_start: 0.8481 (ttt180) cc_final: 0.8195 (ttt180) REVERT: R 995 TYR cc_start: 0.8735 (m-80) cc_final: 0.8240 (m-80) REVERT: R 1014 MET cc_start: 0.4092 (mmp) cc_final: 0.3234 (mpp) REVERT: R 1113 MET cc_start: 0.5290 (ptt) cc_final: 0.4964 (ptt) REVERT: R 1128 ASN cc_start: 0.9057 (m110) cc_final: 0.8717 (m-40) REVERT: R 1146 MET cc_start: 0.9604 (mtp) cc_final: 0.9179 (ptp) REVERT: R 1277 MET cc_start: 0.9534 (mmm) cc_final: 0.9084 (mmp) REVERT: R 1290 TYR cc_start: 0.8809 (m-80) cc_final: 0.8360 (m-10) REVERT: R 1291 MET cc_start: 0.8320 (ttm) cc_final: 0.7545 (pmm) REVERT: R 1304 MET cc_start: 0.8615 (mmm) cc_final: 0.8259 (mmm) REVERT: R 1327 LEU cc_start: 0.8953 (tp) cc_final: 0.8583 (pp) REVERT: S 72 MET cc_start: 0.8370 (mtt) cc_final: 0.8072 (mtm) REVERT: S 285 ILE cc_start: 0.9636 (tp) cc_final: 0.9397 (tp) REVERT: S 729 ILE cc_start: 0.9526 (mt) cc_final: 0.9301 (mm) REVERT: T 142 CYS cc_start: 0.9537 (t) cc_final: 0.8745 (p) REVERT: V 22 GLN cc_start: 0.8878 (tt0) cc_final: 0.8603 (tt0) REVERT: V 111 TYR cc_start: 0.9017 (m-80) cc_final: 0.8740 (m-80) REVERT: V 115 ASN cc_start: 0.9573 (m-40) cc_final: 0.9354 (m110) REVERT: V 217 TYR cc_start: 0.8135 (t80) cc_final: 0.7916 (t80) REVERT: V 231 TRP cc_start: 0.7795 (t-100) cc_final: 0.7477 (t60) REVERT: V 245 HIS cc_start: 0.9458 (m-70) cc_final: 0.9174 (m-70) REVERT: W 64 TYR cc_start: 0.9008 (t80) cc_final: 0.8567 (t80) REVERT: W 85 LEU cc_start: 0.9226 (mp) cc_final: 0.8848 (tp) REVERT: W 87 ILE cc_start: 0.9548 (pt) cc_final: 0.9294 (pt) REVERT: W 90 GLN cc_start: 0.9247 (mp10) cc_final: 0.8833 (mp10) REVERT: W 96 LEU cc_start: 0.8989 (mt) cc_final: 0.8767 (mt) REVERT: Y 160 MET cc_start: 0.8213 (ptt) cc_final: 0.7839 (ptt) outliers start: 1 outliers final: 0 residues processed: 676 average time/residue: 0.4238 time to fit residues: 505.8166 Evaluate side-chains 536 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 676 optimal weight: 3.9990 chunk 712 optimal weight: 3.9990 chunk 650 optimal weight: 0.0870 chunk 693 optimal weight: 10.0000 chunk 417 optimal weight: 40.0000 chunk 302 optimal weight: 0.0970 chunk 544 optimal weight: 0.0570 chunk 212 optimal weight: 3.9990 chunk 626 optimal weight: 7.9990 chunk 655 optimal weight: 0.1980 chunk 690 optimal weight: 10.0000 overall best weight: 0.8876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 686 HIS ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 270 HIS ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 534 HIS S 697 ASN T 123 GLN ** W 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 50316 Z= 0.178 Angle : 0.647 12.377 69242 Z= 0.328 Chirality : 0.043 0.326 8528 Planarity : 0.004 0.086 9242 Dihedral : 4.636 34.990 8063 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 12.25 % Favored : 87.73 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.25 % Twisted General : 0.01 % 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: -1.51 (0.10), residues: 7647 helix: 1.70 (0.09), residues: 3619 sheet: -2.81 (0.24), residues: 418 loop : -3.93 (0.09), residues: 3610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP S 18 HIS 0.013 0.001 HIS J 706 PHE 0.027 0.001 PHE Y 52 TYR 0.051 0.001 TYR R1068 ARG 0.009 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 671 time to evaluate : 4.291 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: H 92 MET cc_start: 0.8939 (ptp) cc_final: 0.8619 (ptp) REVERT: I 312 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8552 (mm-30) REVERT: I 320 MET cc_start: 0.9116 (tpt) cc_final: 0.8846 (tpp) REVERT: I 460 ILE cc_start: 0.8792 (tt) cc_final: 0.8355 (mp) REVERT: I 503 LYS cc_start: 0.9532 (pptt) cc_final: 0.9102 (pttm) REVERT: I 653 MET cc_start: 0.9535 (mtm) cc_final: 0.8847 (mmm) REVERT: I 708 ASP cc_start: 0.9278 (m-30) cc_final: 0.8998 (m-30) REVERT: I 886 ASN cc_start: 0.9380 (t0) cc_final: 0.9133 (t0) REVERT: I 890 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8705 (mmtp) REVERT: J 647 MET cc_start: 0.8987 (tpp) cc_final: 0.8571 (tpp) REVERT: J 670 ASP cc_start: 0.8212 (t0) cc_final: 0.7863 (t0) REVERT: J 757 MET cc_start: 0.9589 (tmm) cc_final: 0.9286 (tmm) REVERT: K 75 LEU cc_start: 0.8046 (tt) cc_final: 0.7744 (tt) REVERT: K 423 LEU cc_start: 0.8813 (tp) cc_final: 0.8089 (pt) REVERT: K 465 LEU cc_start: 0.9716 (mt) cc_final: 0.9366 (mt) REVERT: K 566 ARG cc_start: 0.7734 (tmt170) cc_final: 0.7002 (tmt170) REVERT: K 644 GLU cc_start: 0.8881 (tt0) cc_final: 0.8661 (tt0) REVERT: L 327 ASN cc_start: 0.8146 (t0) cc_final: 0.7797 (t0) REVERT: L 375 LEU cc_start: 0.9557 (mt) cc_final: 0.9263 (mt) REVERT: L 378 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7498 (mmm-85) REVERT: L 383 GLN cc_start: 0.8840 (mm110) cc_final: 0.8440 (mp10) REVERT: L 638 GLU cc_start: 0.8342 (mp0) cc_final: 0.7991 (mp0) REVERT: M 32 LEU cc_start: 0.8957 (mt) cc_final: 0.8555 (mt) REVERT: R 286 MET cc_start: 0.9708 (tmm) cc_final: 0.9349 (tmm) REVERT: R 333 HIS cc_start: 0.9096 (m90) cc_final: 0.8768 (m90) REVERT: R 525 MET cc_start: 0.7331 (mmp) cc_final: 0.6861 (mmp) REVERT: R 574 MET cc_start: 0.0623 (mmm) cc_final: 0.0285 (mmm) REVERT: R 796 MET cc_start: 0.9059 (ptm) cc_final: 0.8815 (ppp) REVERT: R 853 MET cc_start: 0.8652 (ppp) cc_final: 0.8292 (ppp) REVERT: R 871 MET cc_start: 0.9222 (tpt) cc_final: 0.8938 (tpt) REVERT: R 962 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8098 (ttt180) REVERT: R 995 TYR cc_start: 0.8736 (m-80) cc_final: 0.8274 (m-80) REVERT: R 1014 MET cc_start: 0.4257 (mmp) cc_final: 0.3458 (mpp) REVERT: R 1113 MET cc_start: 0.5184 (ptt) cc_final: 0.4918 (ptt) REVERT: R 1128 ASN cc_start: 0.9084 (m110) cc_final: 0.8743 (m110) REVERT: R 1146 MET cc_start: 0.9600 (mtp) cc_final: 0.9176 (ptp) REVERT: R 1277 MET cc_start: 0.9519 (mmm) cc_final: 0.9077 (mmp) REVERT: R 1290 TYR cc_start: 0.8837 (m-80) cc_final: 0.8373 (m-10) REVERT: R 1291 MET cc_start: 0.8274 (ttm) cc_final: 0.7576 (pmm) REVERT: R 1304 MET cc_start: 0.8647 (mmm) cc_final: 0.8170 (mmm) REVERT: R 1327 LEU cc_start: 0.8946 (tp) cc_final: 0.8596 (pp) REVERT: S 72 MET cc_start: 0.8373 (mtt) cc_final: 0.8085 (mtm) REVERT: S 285 ILE cc_start: 0.9614 (tp) cc_final: 0.9384 (tp) REVERT: S 729 ILE cc_start: 0.9517 (mt) cc_final: 0.9298 (mm) REVERT: T 142 CYS cc_start: 0.9502 (t) cc_final: 0.8636 (p) REVERT: V 22 GLN cc_start: 0.8905 (tt0) cc_final: 0.8640 (tt0) REVERT: V 111 TYR cc_start: 0.9008 (m-80) cc_final: 0.8758 (m-80) REVERT: V 231 TRP cc_start: 0.7792 (t-100) cc_final: 0.7558 (t60) REVERT: V 245 HIS cc_start: 0.9464 (m-70) cc_final: 0.9192 (m-70) REVERT: W 64 TYR cc_start: 0.9081 (t80) cc_final: 0.8712 (t80) REVERT: W 85 LEU cc_start: 0.9215 (mp) cc_final: 0.8805 (tp) REVERT: W 90 GLN cc_start: 0.9252 (mp10) cc_final: 0.8903 (mp10) REVERT: Y 160 MET cc_start: 0.8183 (ptt) cc_final: 0.7831 (ptt) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.4342 time to fit residues: 518.1971 Evaluate side-chains 535 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 455 optimal weight: 20.0000 chunk 733 optimal weight: 0.5980 chunk 447 optimal weight: 7.9990 chunk 347 optimal weight: 20.0000 chunk 509 optimal weight: 0.9990 chunk 769 optimal weight: 9.9990 chunk 707 optimal weight: 3.9990 chunk 612 optimal weight: 0.3980 chunk 63 optimal weight: 6.9990 chunk 473 optimal weight: 0.9990 chunk 375 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 686 HIS ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 534 HIS ** S 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 697 ASN ** W 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 50316 Z= 0.177 Angle : 0.645 12.405 69242 Z= 0.326 Chirality : 0.042 0.315 8528 Planarity : 0.004 0.089 9242 Dihedral : 4.566 35.102 8063 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 12.92 % Favored : 87.07 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.25 % Twisted General : 0.01 % 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: -1.45 (0.10), residues: 7647 helix: 1.73 (0.09), residues: 3636 sheet: -2.80 (0.23), residues: 427 loop : -3.89 (0.09), residues: 3584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP S 590 HIS 0.012 0.001 HIS J 706 PHE 0.023 0.001 PHE J 635 TYR 0.046 0.001 TYR R1068 ARG 0.006 0.000 ARG V 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15294 Ramachandran restraints generated. 7647 Oldfield, 0 Emsley, 7647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 4.297 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: H 92 MET cc_start: 0.9018 (ptp) cc_final: 0.8810 (ptm) REVERT: I 312 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8621 (mm-30) REVERT: I 320 MET cc_start: 0.9115 (tpt) cc_final: 0.8850 (tpp) REVERT: I 460 ILE cc_start: 0.8822 (tt) cc_final: 0.8355 (mp) REVERT: I 503 LYS cc_start: 0.9536 (pptt) cc_final: 0.9132 (pttm) REVERT: I 653 MET cc_start: 0.9531 (mtm) cc_final: 0.8968 (mmm) REVERT: I 708 ASP cc_start: 0.9291 (m-30) cc_final: 0.9009 (m-30) REVERT: I 886 ASN cc_start: 0.9396 (t0) cc_final: 0.9157 (t0) REVERT: I 890 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8841 (mmtp) REVERT: J 647 MET cc_start: 0.8976 (tpp) cc_final: 0.8271 (tpp) REVERT: J 651 HIS cc_start: 0.9156 (m90) cc_final: 0.8834 (m90) REVERT: J 670 ASP cc_start: 0.8235 (t0) cc_final: 0.7877 (t0) REVERT: J 757 MET cc_start: 0.9607 (tmm) cc_final: 0.9299 (tmm) REVERT: K 75 LEU cc_start: 0.8061 (tt) cc_final: 0.7781 (tt) REVERT: K 423 LEU cc_start: 0.8911 (tp) cc_final: 0.8187 (pt) REVERT: K 465 LEU cc_start: 0.9714 (mt) cc_final: 0.9361 (mt) REVERT: K 566 ARG cc_start: 0.7741 (tmt170) cc_final: 0.6977 (tmt170) REVERT: K 641 MET cc_start: 0.8680 (ttt) cc_final: 0.8231 (ppp) REVERT: K 644 GLU cc_start: 0.8909 (tt0) cc_final: 0.8693 (tt0) REVERT: L 327 ASN cc_start: 0.8180 (t0) cc_final: 0.7894 (t0) REVERT: L 375 LEU cc_start: 0.9548 (mt) cc_final: 0.9290 (mt) REVERT: L 378 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7486 (mmm-85) REVERT: L 383 GLN cc_start: 0.8883 (mm110) cc_final: 0.8479 (mp10) REVERT: L 638 GLU cc_start: 0.8315 (mp0) cc_final: 0.8016 (mp0) REVERT: M 32 LEU cc_start: 0.8964 (mt) cc_final: 0.8543 (mt) REVERT: R 286 MET cc_start: 0.9711 (tmm) cc_final: 0.9467 (tmm) REVERT: R 333 HIS cc_start: 0.9060 (m90) cc_final: 0.8737 (m90) REVERT: R 525 MET cc_start: 0.7305 (mmp) cc_final: 0.6087 (mmp) REVERT: R 574 MET cc_start: 0.0493 (mmm) cc_final: 0.0214 (mmm) REVERT: R 796 MET cc_start: 0.9058 (ptm) cc_final: 0.8810 (ppp) REVERT: R 853 MET cc_start: 0.8654 (ppp) cc_final: 0.8287 (ppp) REVERT: R 871 MET cc_start: 0.9225 (tpt) cc_final: 0.8943 (tpt) REVERT: R 962 ARG cc_start: 0.8398 (ttt180) cc_final: 0.8064 (ttt180) REVERT: R 995 TYR cc_start: 0.8761 (m-80) cc_final: 0.8300 (m-80) REVERT: R 1014 MET cc_start: 0.4426 (mmp) cc_final: 0.3573 (mpp) REVERT: R 1113 MET cc_start: 0.5141 (ptt) cc_final: 0.4932 (ptt) REVERT: R 1128 ASN cc_start: 0.9117 (m110) cc_final: 0.8797 (m110) REVERT: R 1146 MET cc_start: 0.9599 (mtp) cc_final: 0.9184 (ptp) REVERT: R 1190 LEU cc_start: 0.9393 (tt) cc_final: 0.8966 (tt) REVERT: R 1277 MET cc_start: 0.9514 (mmm) cc_final: 0.8978 (mmm) REVERT: R 1290 TYR cc_start: 0.8891 (m-80) cc_final: 0.8379 (m-10) REVERT: R 1291 MET cc_start: 0.8290 (ttm) cc_final: 0.7634 (pmm) REVERT: R 1304 MET cc_start: 0.8626 (mmm) cc_final: 0.8110 (mmm) REVERT: R 1327 LEU cc_start: 0.8978 (tp) cc_final: 0.8662 (pp) REVERT: S 72 MET cc_start: 0.8374 (mtt) cc_final: 0.8066 (mtm) REVERT: S 267 LEU cc_start: 0.9302 (mt) cc_final: 0.9017 (mt) REVERT: S 285 ILE cc_start: 0.9621 (tp) cc_final: 0.9369 (tp) REVERT: S 729 ILE cc_start: 0.9529 (mt) cc_final: 0.9303 (mm) REVERT: T 142 CYS cc_start: 0.9534 (t) cc_final: 0.8771 (p) REVERT: V 22 GLN cc_start: 0.8916 (tt0) cc_final: 0.8646 (tt0) REVERT: V 111 TYR cc_start: 0.9050 (m-80) cc_final: 0.8788 (m-80) REVERT: V 245 HIS cc_start: 0.9460 (m-70) cc_final: 0.9189 (m-70) REVERT: W 64 TYR cc_start: 0.9141 (t80) cc_final: 0.8798 (t80) REVERT: W 85 LEU cc_start: 0.9210 (mp) cc_final: 0.8752 (tp) REVERT: W 90 GLN cc_start: 0.9222 (mp10) cc_final: 0.8867 (mp10) REVERT: X 79 GLN cc_start: 0.9266 (mm110) cc_final: 0.9008 (tm-30) REVERT: Y 160 MET cc_start: 0.8164 (ptt) cc_final: 0.7830 (ptt) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.4443 time to fit residues: 526.1105 Evaluate side-chains 546 residues out of total 6985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 486 optimal weight: 40.0000 chunk 652 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 564 optimal weight: 7.9990 chunk 90 optimal weight: 30.0000 chunk 170 optimal weight: 9.9990 chunk 613 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 629 optimal weight: 9.9990 chunk 77 optimal weight: 50.0000 chunk 112 optimal weight: 0.2980 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1188 ASN ** J 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 270 HIS ** L 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 70 GLN ** R 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 697 ASN S 834 HIS ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.077661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054071 restraints weight = 352771.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.054920 restraints weight = 264787.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055329 restraints weight = 196523.587| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 50316 Z= 0.364 Angle : 0.818 16.959 69242 Z= 0.432 Chirality : 0.047 0.363 8528 Planarity : 0.006 0.143 9242 Dihedral : 5.615 39.295 8063 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 16.22 % Favored : 83.76 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.25 % Cis-general : 0.10 % Twisted Proline : 0.25 % Twisted General : 0.10 % 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: -1.97 (0.10), residues: 7647 helix: 1.20 (0.09), residues: 3611 sheet: -3.20 (0.22), residues: 454 loop : -3.98 (0.09), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP V 231 HIS 0.017 0.003 HIS R 925 PHE 0.040 0.003 PHE K 208 TYR 0.050 0.003 TYR I 555 ARG 0.012 0.001 ARG J 631 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10221.92 seconds wall clock time: 176 minutes 27.42 seconds (10587.42 seconds total)