Starting phenix.real_space_refine on Sun Oct 13 13:06:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gaw_51190/10_2024/9gaw_51190.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gaw_51190/10_2024/9gaw_51190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gaw_51190/10_2024/9gaw_51190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gaw_51190/10_2024/9gaw_51190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gaw_51190/10_2024/9gaw_51190.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gaw_51190/10_2024/9gaw_51190.cif" } resolution = 2.9 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= 0.021 sd= 0.103 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 394 5.16 5 C 42564 2.51 5 N 11412 2.21 5 O 12264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 66640 Number of models: 1 Model: "" Number of chains: 24 Chain: "L" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1404 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 446 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 50} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 50} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 452 Chain: "A" Number of atoms: 12378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1602, 12378 Classifications: {'peptide': 1602} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 2, 'PTRANS': 87, 'TRANS': 1512} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 178 Chain: "N" Number of atoms: 4632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 4632 Classifications: {'peptide': 632} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 28, 'TRANS': 603} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 538 Unresolved non-hydrogen angles: 668 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 11, 'TYR:plan': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 28, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 351 Chain: "I" Number of atoms: 5675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5675 Classifications: {'peptide': 721} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 696} Chain breaks: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "O" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5473 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 679} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "S" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 655 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 4164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4164 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 501} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 221 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 222 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 514 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 469 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3957 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "P" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3929 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 475} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Q" Number of atoms: 4064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 505, 4056 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 490} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 505, 4056 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 490} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 4145 Chain: "Y" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3696 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 15, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 12, 'ARG:plan': 8, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 121 Chain: "U" Number of atoms: 3888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3888 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 12, 'TRANS': 475} Chain breaks: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "V" Number of atoms: 4012 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 493, 4004 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 479} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 493, 4004 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 479} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 4088 Chain: "R" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3015 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 14, 'TRANS': 400} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 308 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 153 Chain: "C" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 573 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "Z" Number of atoms: 3247 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 455, 3245 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 14, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 171 Conformer: "B" Number of residues, atoms: 455, 3245 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 14, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 171 bond proxies already assigned to first conformer: 3290 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15646 SG CYS N 221 67.104 22.552 181.439 1.00 64.17 S ATOM 15661 SG CYS N 224 64.803 22.236 183.768 1.00 30.00 S ATOM 15714 SG CYS N 231 63.687 20.152 182.367 1.00 60.37 S ATOM 15734 SG CYS N 233 63.112 23.449 180.914 1.00 70.18 S ATOM 30291 SG CYS S 378 121.258 63.890 142.888 1.00 93.10 S ATOM 30316 SG CYS S 381 119.830 63.985 139.359 1.00 89.41 S ATOM 30424 SG CYS S 396 121.575 67.071 140.885 1.00 93.57 S ATOM 30455 SG CYS S 401 118.087 65.913 141.972 1.00 92.69 S ATOM 30496 SG CYS S 406 125.921 64.530 155.744 1.00 87.72 S ATOM 30514 SG CYS S 409 124.531 60.824 157.535 1.00 30.00 S ATOM 62969 SG CYS C 23 139.598 61.470 134.693 1.00 84.14 S ATOM 62987 SG CYS C 26 136.126 61.680 136.106 1.00 81.36 S ATOM 63221 SG CYS C 59 136.499 59.978 132.826 1.00 83.13 S ATOM 63046 SG CYS C 34 133.256 55.765 133.561 1.00 80.41 S ATOM 63067 SG CYS C 37 132.424 52.317 133.718 1.00 77.91 S ATOM 63106 SG CYS C 44 135.873 53.867 135.366 1.00 82.92 S ATOM 63157 SG CYS C 51 150.931 63.447 130.537 1.00 78.16 S ATOM 63315 SG CYS C 73 147.434 64.951 129.886 1.00 82.15 S ATOM 63333 SG CYS C 76 150.975 67.137 130.558 1.00 78.79 S Time building chain proxies: 30.07, per 1000 atoms: 0.45 Number of scatterers: 66640 At special positions: 0 Unit cell: (171.2, 209.72, 237.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 394 16.00 O 12264 8.00 N 11412 7.00 C 42564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 12.21 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 101 " pdb="ZN ZN C 101 " - pdb=" ND1 HIS C 56 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 26 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 59 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 23 " pdb=" ZN C 102 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 44 " pdb="ZN ZN C 102 " - pdb=" ND1 HIS C 58 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 37 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 34 " pdb=" ZN C 103 " pdb="ZN ZN C 103 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 103 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 103 " - pdb=" ND1 HIS C 53 " pdb="ZN ZN C 103 " - pdb=" SG CYS C 51 " pdb=" ZN N 901 " pdb="ZN ZN N 901 " - pdb=" SG CYS N 224 " pdb="ZN ZN N 901 " - pdb=" SG CYS N 221 " pdb="ZN ZN N 901 " - pdb=" SG CYS N 231 " pdb="ZN ZN N 901 " - pdb=" SG CYS N 233 " pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 381 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 401 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 378 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 396 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 414 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 406 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 409 " Number of angles added : 21 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16438 Finding SS restraints... Secondary structure from input PDB file: 421 helices and 36 sheets defined 67.2% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.60 Creating SS restraints... Processing helix chain 'L' and resid 12 through 19 removed outlier: 3.672A pdb=" N LEU L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 removed outlier: 3.578A pdb=" N LEU L 45 " --> pdb=" O GLY L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 175 through 180 Processing helix chain 'D' and resid 27 through 46 Processing helix chain 'A' and resid 22 through 30 removed outlier: 4.035A pdb=" N ASP A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 630 through 646 Processing helix chain 'A' and resid 655 through 667 Processing helix chain 'A' and resid 675 through 680 removed outlier: 4.261A pdb=" N ASN A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 722 removed outlier: 3.618A pdb=" N VAL A 719 " --> pdb=" O TYR A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 774 Processing helix chain 'A' and resid 775 through 780 removed outlier: 6.222A pdb=" N LEU A 778 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 797 removed outlier: 4.159A pdb=" N GLU A 788 " --> pdb=" O CYS A 784 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 824 through 829 removed outlier: 4.284A pdb=" N GLY A 829 " --> pdb=" O PRO A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 854 Processing helix chain 'A' and resid 867 through 881 Processing helix chain 'A' and resid 884 through 890 removed outlier: 3.996A pdb=" N VAL A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 938 Processing helix chain 'A' and resid 940 through 947 Processing helix chain 'A' and resid 952 through 965 Processing helix chain 'A' and resid 971 through 979 Processing helix chain 'A' and resid 980 through 984 removed outlier: 3.563A pdb=" N LEU A 983 " --> pdb=" O ARG A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1058 through 1078 removed outlier: 3.761A pdb=" N ARG A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.453A pdb=" N GLY A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 Processing helix chain 'A' and resid 1154 through 1161 Processing helix chain 'A' and resid 1168 through 1183 Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 3.508A pdb=" N LYS A1187 " --> pdb=" O HIS A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1200 removed outlier: 3.844A pdb=" N GLY A1200 " --> pdb=" O TYR A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1217 Processing helix chain 'A' and resid 1221 through 1230 Processing helix chain 'A' and resid 1246 through 1261 Processing helix chain 'A' and resid 1266 through 1278 removed outlier: 3.973A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 Processing helix chain 'A' and resid 1320 through 1331 Processing helix chain 'A' and resid 1359 through 1375 Proline residue: A1365 - end of helix Processing helix chain 'A' and resid 1380 through 1386 removed outlier: 3.649A pdb=" N TRP A1386 " --> pdb=" O SER A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1397 Processing helix chain 'A' and resid 1400 through 1415 removed outlier: 3.511A pdb=" N LEU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1429 removed outlier: 3.705A pdb=" N ASN A1429 " --> pdb=" O TRP A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1438 Processing helix chain 'A' and resid 1453 through 1476 Processing helix chain 'A' and resid 1481 through 1500 Processing helix chain 'A' and resid 1503 through 1508 Processing helix chain 'A' and resid 1508 through 1527 Processing helix chain 'A' and resid 1532 through 1545 Processing helix chain 'A' and resid 1551 through 1566 Processing helix chain 'A' and resid 1567 through 1570 Processing helix chain 'A' and resid 1577 through 1588 Processing helix chain 'A' and resid 1603 through 1612 removed outlier: 4.481A pdb=" N TYR A1610 " --> pdb=" O ARG A1607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A1611 " --> pdb=" O HIS A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1661 No H-bonds generated for 'chain 'A' and resid 1659 through 1661' Processing helix chain 'A' and resid 1684 through 1693 Processing helix chain 'A' and resid 1725 through 1733 removed outlier: 3.700A pdb=" N GLU A1729 " --> pdb=" O ASN A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1741 removed outlier: 4.533A pdb=" N SER A1739 " --> pdb=" O GLU A1736 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1754 Processing helix chain 'A' and resid 1763 through 1781 removed outlier: 4.288A pdb=" N ILE A1767 " --> pdb=" O GLN A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1785 No H-bonds generated for 'chain 'A' and resid 1783 through 1785' Processing helix chain 'A' and resid 1786 through 1802 Processing helix chain 'A' and resid 1808 through 1821 Processing helix chain 'A' and resid 1824 through 1830 removed outlier: 4.139A pdb=" N GLU A1828 " --> pdb=" O ARG A1824 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1863 removed outlier: 3.587A pdb=" N LEU A1860 " --> pdb=" O LEU A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1874 removed outlier: 3.865A pdb=" N CYS A1867 " --> pdb=" O GLY A1863 " (cutoff:3.500A) Processing helix chain 'A' and resid 1878 through 1880 No H-bonds generated for 'chain 'A' and resid 1878 through 1880' Processing helix chain 'A' and resid 1881 through 1893 Processing helix chain 'A' and resid 1896 through 1900 Processing helix chain 'A' and resid 1910 through 1920 removed outlier: 4.220A pdb=" N GLN A1920 " --> pdb=" O PHE A1916 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1936 removed outlier: 3.584A pdb=" N ARG A1930 " --> pdb=" O ARG A1926 " (cutoff:3.500A) Proline residue: A1933 - end of helix Processing helix chain 'N' and resid 18 through 32 Processing helix chain 'N' and resid 56 through 65 removed outlier: 3.780A pdb=" N GLU N 60 " --> pdb=" O ARG N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 69 No H-bonds generated for 'chain 'N' and resid 67 through 69' Processing helix chain 'N' and resid 70 through 86 Processing helix chain 'N' and resid 86 through 100 removed outlier: 3.581A pdb=" N GLU N 90 " --> pdb=" O ASN N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 138 Proline residue: N 124 - end of helix Processing helix chain 'N' and resid 148 through 162 Processing helix chain 'N' and resid 166 through 189 Processing helix chain 'N' and resid 191 through 195 Processing helix chain 'N' and resid 205 through 218 removed outlier: 3.693A pdb=" N TYR N 213 " --> pdb=" O ARG N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 231 Processing helix chain 'N' and resid 232 through 249 removed outlier: 4.205A pdb=" N GLU N 238 " --> pdb=" O ARG N 234 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS N 241 " --> pdb=" O LEU N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 257 Processing helix chain 'N' and resid 257 through 278 Processing helix chain 'N' and resid 285 through 304 Processing helix chain 'N' and resid 319 through 343 Processing helix chain 'N' and resid 343 through 350 removed outlier: 3.714A pdb=" N ASP N 350 " --> pdb=" O SER N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 366 Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 370 through 386 Processing helix chain 'N' and resid 392 through 411 Processing helix chain 'N' and resid 414 through 431 removed outlier: 3.554A pdb=" N GLU N 422 " --> pdb=" O GLU N 418 " (cutoff:3.500A) Proline residue: N 423 - end of helix Processing helix chain 'N' and resid 433 through 442 Processing helix chain 'N' and resid 450 through 458 Processing helix chain 'N' and resid 476 through 480 removed outlier: 3.867A pdb=" N TRP N 480 " --> pdb=" O PRO N 477 " (cutoff:3.500A) Processing helix chain 'N' and resid 500 through 510 removed outlier: 4.155A pdb=" N TYR N 509 " --> pdb=" O LEU N 505 " (cutoff:3.500A) Processing helix chain 'N' and resid 511 through 530 Processing helix chain 'N' and resid 534 through 550 Processing helix chain 'N' and resid 554 through 581 removed outlier: 3.518A pdb=" N MET N 560 " --> pdb=" O PHE N 556 " (cutoff:3.500A) Processing helix chain 'N' and resid 612 through 630 Processing helix chain 'N' and resid 660 through 671 Processing helix chain 'N' and resid 677 through 686 Processing helix chain 'N' and resid 688 through 703 removed outlier: 4.285A pdb=" N VAL N 698 " --> pdb=" O ARG N 694 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP N 699 " --> pdb=" O ARG N 695 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 160 through 170 removed outlier: 4.009A pdb=" N ILE I 164 " --> pdb=" O ASN I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 244 Processing helix chain 'I' and resid 244 through 276 Processing helix chain 'I' and resid 277 through 280 Processing helix chain 'I' and resid 281 through 294 Processing helix chain 'I' and resid 299 through 311 Processing helix chain 'I' and resid 314 through 323 Processing helix chain 'I' and resid 326 through 371 removed outlier: 4.431A pdb=" N GLN I 353 " --> pdb=" O ILE I 349 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER I 354 " --> pdb=" O SER I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 377 Processing helix chain 'I' and resid 378 through 380 No H-bonds generated for 'chain 'I' and resid 378 through 380' Processing helix chain 'I' and resid 382 through 429 Processing helix chain 'I' and resid 441 through 456 Processing helix chain 'I' and resid 475 through 480 Processing helix chain 'I' and resid 495 through 504 Processing helix chain 'I' and resid 521 through 548 Proline residue: I 540 - end of helix removed outlier: 3.667A pdb=" N MET I 548 " --> pdb=" O ILE I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 671 through 675 Processing helix chain 'O' and resid 31 through 46 Processing helix chain 'O' and resid 54 through 70 removed outlier: 3.980A pdb=" N ARG O 59 " --> pdb=" O MET O 55 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU O 65 " --> pdb=" O ASN O 61 " (cutoff:3.500A) Proline residue: O 66 - end of helix Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'O' and resid 86 through 103 removed outlier: 3.836A pdb=" N ALA O 90 " --> pdb=" O CYS O 86 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN O 91 " --> pdb=" O PRO O 87 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER O 92 " --> pdb=" O GLN O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 118 removed outlier: 3.669A pdb=" N MET O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 145 Processing helix chain 'O' and resid 147 through 167 Processing helix chain 'O' and resid 208 through 226 Processing helix chain 'O' and resid 232 through 247 Processing helix chain 'O' and resid 250 through 264 removed outlier: 3.742A pdb=" N HIS O 254 " --> pdb=" O PHE O 250 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL O 264 " --> pdb=" O ASN O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 281 Processing helix chain 'O' and resid 288 through 292 Processing helix chain 'O' and resid 298 through 315 removed outlier: 4.169A pdb=" N TYR O 302 " --> pdb=" O ARG O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 334 removed outlier: 3.696A pdb=" N GLU O 326 " --> pdb=" O LEU O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 351 Processing helix chain 'O' and resid 357 through 370 Processing helix chain 'O' and resid 373 through 392 Processing helix chain 'O' and resid 394 through 412 removed outlier: 3.740A pdb=" N ASP O 404 " --> pdb=" O ASP O 400 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER O 405 " --> pdb=" O ALA O 401 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU O 408 " --> pdb=" O ASP O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 432 Processing helix chain 'O' and resid 434 through 447 Processing helix chain 'O' and resid 463 through 480 Processing helix chain 'O' and resid 482 through 497 Processing helix chain 'O' and resid 503 through 522 removed outlier: 4.347A pdb=" N TRP O 507 " --> pdb=" O HIS O 503 " (cutoff:3.500A) Processing helix chain 'O' and resid 524 through 539 removed outlier: 3.863A pdb=" N THR O 533 " --> pdb=" O ASP O 529 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) Processing helix chain 'O' and resid 539 through 554 Processing helix chain 'O' and resid 556 through 575 removed outlier: 3.582A pdb=" N ALA O 560 " --> pdb=" O GLN O 556 " (cutoff:3.500A) Processing helix chain 'O' and resid 576 through 592 Processing helix chain 'O' and resid 596 through 599 Processing helix chain 'O' and resid 600 through 615 Processing helix chain 'O' and resid 616 through 635 Processing helix chain 'O' and resid 636 through 648 removed outlier: 3.741A pdb=" N MET O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) Processing helix chain 'O' and resid 648 through 654 Processing helix chain 'O' and resid 656 through 675 Processing helix chain 'O' and resid 676 through 678 No H-bonds generated for 'chain 'O' and resid 676 through 678' Processing helix chain 'O' and resid 679 through 705 removed outlier: 3.579A pdb=" N VAL O 704 " --> pdb=" O TYR O 700 " (cutoff:3.500A) Processing helix chain 'O' and resid 706 through 725 Processing helix chain 'O' and resid 726 through 742 Processing helix chain 'S' and resid 359 through 367 Processing helix chain 'S' and resid 437 through 447 removed outlier: 4.025A pdb=" N ARG S 446 " --> pdb=" O LYS S 442 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU S 447 " --> pdb=" O ASN S 443 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'K' and resid 19 through 33 removed outlier: 4.043A pdb=" N TRP K 25 " --> pdb=" O SER K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 62 removed outlier: 3.699A pdb=" N LEU K 60 " --> pdb=" O ALA K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 85 through 95 Processing helix chain 'K' and resid 128 through 143 Processing helix chain 'K' and resid 145 through 160 Processing helix chain 'K' and resid 163 through 171 Processing helix chain 'K' and resid 177 through 188 Processing helix chain 'K' and resid 189 through 193 removed outlier: 3.960A pdb=" N LYS K 192 " --> pdb=" O PRO K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 210 Processing helix chain 'K' and resid 214 through 218 removed outlier: 3.582A pdb=" N THR K 218 " --> pdb=" O PRO K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 229 removed outlier: 3.663A pdb=" N GLU K 229 " --> pdb=" O GLY K 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 226 through 229' Processing helix chain 'K' and resid 230 through 244 Processing helix chain 'K' and resid 246 through 261 Processing helix chain 'K' and resid 266 through 278 removed outlier: 4.704A pdb=" N VAL K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 298 through 313 removed outlier: 4.143A pdb=" N TRP K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 Processing helix chain 'K' and resid 333 through 347 removed outlier: 4.214A pdb=" N GLU K 347 " --> pdb=" O SER K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 364 Processing helix chain 'K' and resid 368 through 381 Processing helix chain 'K' and resid 383 through 398 removed outlier: 3.907A pdb=" N ARG K 389 " --> pdb=" O LYS K 385 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE K 390 " --> pdb=" O LEU K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 416 Processing helix chain 'K' and resid 417 through 435 Processing helix chain 'K' and resid 440 through 443 Processing helix chain 'K' and resid 444 through 458 removed outlier: 3.591A pdb=" N LEU K 448 " --> pdb=" O TRP K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 475 removed outlier: 3.507A pdb=" N VAL K 473 " --> pdb=" O ARG K 469 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU K 474 " --> pdb=" O GLN K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 492 Processing helix chain 'K' and resid 496 through 509 Processing helix chain 'K' and resid 512 through 528 Processing helix chain 'K' and resid 554 through 560 Processing helix chain 'G' and resid 12 through 14 No H-bonds generated for 'chain 'G' and resid 12 through 14' Processing helix chain 'G' and resid 15 through 26 removed outlier: 4.273A pdb=" N PHE G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 14 No H-bonds generated for 'chain 'W' and resid 12 through 14' Processing helix chain 'W' and resid 15 through 26 removed outlier: 4.262A pdb=" N PHE W 19 " --> pdb=" O ASP W 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 15 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 49 through 55 Processing helix chain 'M' and resid 61 through 65 removed outlier: 4.017A pdb=" N TYR M 64 " --> pdb=" O ALA M 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 84 Processing helix chain 'H' and resid 86 through 92 removed outlier: 4.420A pdb=" N GLU H 90 " --> pdb=" O VAL H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 Processing helix chain 'H' and resid 98 through 103 Processing helix chain 'J' and resid 6 through 18 Processing helix chain 'J' and resid 20 through 36 Processing helix chain 'J' and resid 37 through 51 removed outlier: 3.546A pdb=" N LEU J 41 " --> pdb=" O SER J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 64 removed outlier: 3.554A pdb=" N ALA J 57 " --> pdb=" O LYS J 53 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 82 Processing helix chain 'J' and resid 84 through 94 Processing helix chain 'J' and resid 102 through 111 removed outlier: 3.595A pdb=" N VAL J 107 " --> pdb=" O HIS J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 128 Processing helix chain 'J' and resid 130 through 145 Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 163 through 168 Processing helix chain 'J' and resid 452 through 478 removed outlier: 4.797A pdb=" N GLY J 461 " --> pdb=" O ALA J 457 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU J 462 " --> pdb=" O ALA J 458 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU J 468 " --> pdb=" O SER J 464 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET J 469 " --> pdb=" O LEU J 465 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 490 removed outlier: 3.564A pdb=" N HIS J 490 " --> pdb=" O ASN J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 497 Processing helix chain 'J' and resid 498 through 513 Processing helix chain 'J' and resid 514 through 529 Processing helix chain 'J' and resid 535 through 547 Processing helix chain 'J' and resid 548 through 563 Processing helix chain 'J' and resid 566 through 579 removed outlier: 3.650A pdb=" N TRP J 570 " --> pdb=" O SER J 566 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 597 Processing helix chain 'J' and resid 600 through 614 removed outlier: 3.795A pdb=" N TYR J 604 " --> pdb=" O TYR J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 616 through 631 Processing helix chain 'J' and resid 634 through 648 removed outlier: 3.737A pdb=" N TRP J 638 " --> pdb=" O HIS J 634 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 665 Processing helix chain 'J' and resid 668 through 682 Processing helix chain 'J' and resid 684 through 699 Processing helix chain 'J' and resid 702 through 716 Processing helix chain 'J' and resid 718 through 733 removed outlier: 3.641A pdb=" N GLU J 728 " --> pdb=" O GLN J 724 " (cutoff:3.500A) Processing helix chain 'J' and resid 736 through 751 removed outlier: 3.747A pdb=" N TYR J 740 " --> pdb=" O GLU J 736 " (cutoff:3.500A) Processing helix chain 'J' and resid 752 through 767 removed outlier: 3.577A pdb=" N ASP J 767 " --> pdb=" O ALA J 763 " (cutoff:3.500A) Processing helix chain 'J' and resid 772 through 780 Processing helix chain 'P' and resid 6 through 18 Processing helix chain 'P' and resid 20 through 35 Processing helix chain 'P' and resid 37 through 51 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'P' and resid 84 through 93 Processing helix chain 'P' and resid 102 through 111 Processing helix chain 'P' and resid 113 through 128 removed outlier: 3.510A pdb=" N THR P 117 " --> pdb=" O SER P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 145 Processing helix chain 'P' and resid 149 through 159 Processing helix chain 'P' and resid 163 through 168 Processing helix chain 'P' and resid 449 through 478 removed outlier: 3.666A pdb=" N LEU P 454 " --> pdb=" O GLN P 450 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY P 461 " --> pdb=" O ALA P 457 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU P 462 " --> pdb=" O ALA P 458 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU P 465 " --> pdb=" O GLY P 461 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG P 467 " --> pdb=" O MET P 463 " (cutoff:3.500A) Processing helix chain 'P' and resid 480 through 490 removed outlier: 3.746A pdb=" N HIS P 490 " --> pdb=" O ASN P 486 " (cutoff:3.500A) Processing helix chain 'P' and resid 492 through 497 Processing helix chain 'P' and resid 498 through 512 Processing helix chain 'P' and resid 514 through 529 Processing helix chain 'P' and resid 535 through 547 Processing helix chain 'P' and resid 548 through 561 Processing helix chain 'P' and resid 566 through 580 removed outlier: 3.768A pdb=" N TRP P 570 " --> pdb=" O SER P 566 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN P 580 " --> pdb=" O CYS P 576 " (cutoff:3.500A) Processing helix chain 'P' and resid 582 through 597 Processing helix chain 'P' and resid 600 through 614 removed outlier: 3.691A pdb=" N TYR P 604 " --> pdb=" O TYR P 600 " (cutoff:3.500A) Processing helix chain 'P' and resid 616 through 631 Processing helix chain 'P' and resid 634 through 648 removed outlier: 3.682A pdb=" N TRP P 638 " --> pdb=" O HIS P 634 " (cutoff:3.500A) Processing helix chain 'P' and resid 650 through 663 Processing helix chain 'P' and resid 668 through 682 Processing helix chain 'P' and resid 684 through 699 Processing helix chain 'P' and resid 702 through 716 removed outlier: 4.157A pdb=" N LYS P 706 " --> pdb=" O ASN P 702 " (cutoff:3.500A) Processing helix chain 'P' and resid 718 through 733 Processing helix chain 'P' and resid 736 through 751 removed outlier: 3.867A pdb=" N TYR P 740 " --> pdb=" O GLU P 736 " (cutoff:3.500A) Processing helix chain 'P' and resid 752 through 767 Processing helix chain 'Q' and resid 2 through 16 Processing helix chain 'Q' and resid 18 through 33 Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 62 Processing helix chain 'Q' and resid 64 through 68 Processing helix chain 'Q' and resid 69 through 83 Processing helix chain 'Q' and resid 85 through 94 Processing helix chain 'Q' and resid 125 through 143 Processing helix chain 'Q' and resid 145 through 160 removed outlier: 3.884A pdb=" N TYR Q 151 " --> pdb=" O THR Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 173 removed outlier: 3.675A pdb=" N PHE Q 167 " --> pdb=" O CYS Q 163 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS Q 173 " --> pdb=" O LEU Q 169 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 188 Processing helix chain 'Q' and resid 194 through 207 Processing helix chain 'Q' and resid 232 through 244 Processing helix chain 'Q' and resid 246 through 259 removed outlier: 3.858A pdb=" N VAL Q 256 " --> pdb=" O LYS Q 252 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL Q 257 " --> pdb=" O LEU Q 253 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 279 removed outlier: 4.513A pdb=" N VAL Q 270 " --> pdb=" O SER Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 295 Processing helix chain 'Q' and resid 298 through 313 removed outlier: 3.812A pdb=" N TRP Q 302 " --> pdb=" O ASN Q 298 " (cutoff:3.500A) Processing helix chain 'Q' and resid 315 through 330 Processing helix chain 'Q' and resid 333 through 346 removed outlier: 4.005A pdb=" N TRP Q 337 " --> pdb=" O TYR Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 364 Processing helix chain 'Q' and resid 368 through 381 Processing helix chain 'Q' and resid 383 through 398 Processing helix chain 'Q' and resid 401 through 416 Processing helix chain 'Q' and resid 417 through 433 Processing helix chain 'Q' and resid 441 through 443 No H-bonds generated for 'chain 'Q' and resid 441 through 443' Processing helix chain 'Q' and resid 444 through 458 removed outlier: 3.716A pdb=" N LEU Q 448 " --> pdb=" O TRP Q 444 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 475 Processing helix chain 'Q' and resid 478 through 493 Processing helix chain 'Q' and resid 494 through 509 Processing helix chain 'Q' and resid 513 through 529 Processing helix chain 'Y' and resid 36 through 48 Processing helix chain 'Y' and resid 49 through 67 removed outlier: 3.523A pdb=" N LEU Y 55 " --> pdb=" O SER Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 72 through 89 Processing helix chain 'Y' and resid 92 through 109 removed outlier: 3.521A pdb=" N ALA Y 96 " --> pdb=" O GLU Y 92 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 149 removed outlier: 3.931A pdb=" N VAL Y 138 " --> pdb=" O SER Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 162 removed outlier: 3.777A pdb=" N ILE Y 162 " --> pdb=" O ILE Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 168 through 183 Processing helix chain 'Y' and resid 185 through 199 Processing helix chain 'Y' and resid 202 through 212 Processing helix chain 'Y' and resid 215 through 223 removed outlier: 3.711A pdb=" N VAL Y 219 " --> pdb=" O LYS Y 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 230 removed outlier: 3.846A pdb=" N ILE Y 227 " --> pdb=" O THR Y 223 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN Y 228 " --> pdb=" O MET Y 224 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 249 Processing helix chain 'Y' and resid 250 through 264 Processing helix chain 'Y' and resid 270 through 285 Processing helix chain 'Y' and resid 288 through 301 Processing helix chain 'Y' and resid 307 through 318 Processing helix chain 'Y' and resid 320 through 335 Processing helix chain 'Y' and resid 338 through 352 removed outlier: 4.563A pdb=" N TRP Y 342 " --> pdb=" O HIS Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 369 Processing helix chain 'Y' and resid 372 through 387 Processing helix chain 'Y' and resid 388 through 403 Processing helix chain 'Y' and resid 406 through 420 removed outlier: 3.831A pdb=" N TYR Y 410 " --> pdb=" O ARG Y 406 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 438 removed outlier: 3.540A pdb=" N ALA Y 426 " --> pdb=" O SER Y 422 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET Y 427 " --> pdb=" O ILE Y 423 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL Y 428 " --> pdb=" O ARG Y 424 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N MET Y 429 " --> pdb=" O GLU Y 425 " (cutoff:3.500A) Processing helix chain 'Y' and resid 440 through 453 removed outlier: 4.036A pdb=" N GLU Y 453 " --> pdb=" O THR Y 449 " (cutoff:3.500A) Processing helix chain 'Y' and resid 457 through 472 removed outlier: 4.012A pdb=" N LYS Y 467 " --> pdb=" O THR Y 463 " (cutoff:3.500A) Processing helix chain 'Y' and resid 475 through 490 Processing helix chain 'Y' and resid 492 through 504 Processing helix chain 'Y' and resid 508 through 523 Processing helix chain 'Y' and resid 524 through 539 Processing helix chain 'Y' and resid 542 through 554 Processing helix chain 'U' and resid 28 through 47 Processing helix chain 'U' and resid 48 through 62 removed outlier: 3.529A pdb=" N SER U 61 " --> pdb=" O GLU U 57 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 83 Processing helix chain 'U' and resid 83 through 96 Processing helix chain 'U' and resid 98 through 106 Processing helix chain 'U' and resid 111 through 133 Processing helix chain 'U' and resid 148 through 164 Processing helix chain 'U' and resid 168 through 182 Processing helix chain 'U' and resid 184 through 199 removed outlier: 3.685A pdb=" N ASP U 190 " --> pdb=" O LYS U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 213 removed outlier: 3.988A pdb=" N TRP U 206 " --> pdb=" O HIS U 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 215 through 221 removed outlier: 3.921A pdb=" N LEU U 219 " --> pdb=" O ASP U 215 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 241 removed outlier: 3.996A pdb=" N PHE U 232 " --> pdb=" O TRP U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 243 through 258 Processing helix chain 'U' and resid 262 through 276 Processing helix chain 'U' and resid 278 through 293 Processing helix chain 'U' and resid 299 through 311 Processing helix chain 'U' and resid 312 through 327 Processing helix chain 'U' and resid 330 through 344 Processing helix chain 'U' and resid 346 through 361 Processing helix chain 'U' and resid 364 through 378 removed outlier: 4.509A pdb=" N TRP U 368 " --> pdb=" O TYR U 364 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR U 369 " --> pdb=" O LEU U 365 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 395 Processing helix chain 'U' and resid 398 through 412 Processing helix chain 'U' and resid 416 through 429 Processing helix chain 'U' and resid 432 through 446 removed outlier: 3.663A pdb=" N LEU U 436 " --> pdb=" O ASP U 432 " (cutoff:3.500A) Processing helix chain 'U' and resid 448 through 462 removed outlier: 3.567A pdb=" N ALA U 452 " --> pdb=" O GLN U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 468 through 476 Processing helix chain 'U' and resid 483 through 500 Processing helix chain 'U' and resid 508 through 523 removed outlier: 4.004A pdb=" N LYS U 522 " --> pdb=" O GLN U 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 47 Processing helix chain 'V' and resid 48 through 62 removed outlier: 3.685A pdb=" N SER V 61 " --> pdb=" O GLU V 57 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU V 62 " --> pdb=" O LEU V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 83 removed outlier: 3.728A pdb=" N ASP V 83 " --> pdb=" O GLU V 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 83 through 96 removed outlier: 3.544A pdb=" N VAL V 96 " --> pdb=" O ALA V 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 106 removed outlier: 3.609A pdb=" N PHE V 105 " --> pdb=" O ARG V 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU V 106 " --> pdb=" O ALA V 102 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 136 Processing helix chain 'V' and resid 150 through 164 Processing helix chain 'V' and resid 168 through 182 Processing helix chain 'V' and resid 184 through 199 Processing helix chain 'V' and resid 202 through 213 removed outlier: 4.368A pdb=" N TRP V 206 " --> pdb=" O HIS V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 215 through 222 Processing helix chain 'V' and resid 229 through 241 Processing helix chain 'V' and resid 243 through 258 removed outlier: 3.537A pdb=" N GLY V 258 " --> pdb=" O LEU V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 262 through 277 Processing helix chain 'V' and resid 278 through 293 Processing helix chain 'V' and resid 299 through 311 removed outlier: 3.631A pdb=" N PHE V 303 " --> pdb=" O ASN V 299 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 325 Processing helix chain 'V' and resid 330 through 344 Processing helix chain 'V' and resid 346 through 361 Processing helix chain 'V' and resid 365 through 378 removed outlier: 4.409A pdb=" N THR V 369 " --> pdb=" O LEU V 365 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU V 370 " --> pdb=" O GLY V 366 " (cutoff:3.500A) Processing helix chain 'V' and resid 380 through 395 Processing helix chain 'V' and resid 398 through 412 Processing helix chain 'V' and resid 417 through 429 removed outlier: 4.566A pdb=" N TYR V 421 " --> pdb=" O TYR V 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 432 through 446 removed outlier: 3.957A pdb=" N LEU V 436 " --> pdb=" O ASP V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 462 removed outlier: 3.515A pdb=" N LYS V 454 " --> pdb=" O VAL V 450 " (cutoff:3.500A) Processing helix chain 'V' and resid 468 through 480 Processing helix chain 'V' and resid 482 through 500 removed outlier: 3.991A pdb=" N CYS V 500 " --> pdb=" O ASP V 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 510 through 523 removed outlier: 3.510A pdb=" N TYR V 515 " --> pdb=" O THR V 511 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 13 Processing helix chain 'R' and resid 56 through 63 Processing helix chain 'R' and resid 89 through 100 Processing helix chain 'R' and resid 154 through 162 Processing helix chain 'R' and resid 224 through 229 removed outlier: 3.622A pdb=" N GLU R 228 " --> pdb=" O ASP R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 490 through 495 removed outlier: 3.730A pdb=" N ARG R 494 " --> pdb=" O LEU R 491 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE R 495 " --> pdb=" O PHE R 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 Processing helix chain 'Z' and resid 36 through 48 Processing helix chain 'Z' and resid 50 through 67 removed outlier: 4.483A pdb=" N LEU Z 55 " --> pdb=" O SER Z 51 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU Z 56 " --> pdb=" O ASN Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 90 Processing helix chain 'Z' and resid 93 through 111 Processing helix chain 'Z' and resid 134 through 149 Processing helix chain 'Z' and resid 155 through 160 Processing helix chain 'Z' and resid 163 through 167 Processing helix chain 'Z' and resid 168 through 183 Processing helix chain 'Z' and resid 184 through 199 Processing helix chain 'Z' and resid 202 through 212 Processing helix chain 'Z' and resid 215 through 223 removed outlier: 3.725A pdb=" N VAL Z 219 " --> pdb=" O LYS Z 215 " (cutoff:3.500A) Processing helix chain 'Z' and resid 223 through 230 removed outlier: 3.583A pdb=" N THR Z 229 " --> pdb=" O ASN Z 225 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 249 removed outlier: 4.271A pdb=" N VAL Z 238 " --> pdb=" O ASP Z 234 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE Z 245 " --> pdb=" O LYS Z 241 " (cutoff:3.500A) Processing helix chain 'Z' and resid 250 through 264 Processing helix chain 'Z' and resid 270 through 285 Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.904A pdb=" N GLN Z 298 " --> pdb=" O PHE Z 294 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N MET Z 299 " --> pdb=" O GLU Z 295 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU Z 300 " --> pdb=" O GLN Z 296 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP Z 301 " --> pdb=" O ALA Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 307 through 318 Processing helix chain 'Z' and resid 320 through 335 removed outlier: 3.919A pdb=" N VAL Z 324 " --> pdb=" O ARG Z 320 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU Z 325 " --> pdb=" O LEU Z 321 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN Z 326 " --> pdb=" O GLU Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 338 through 351 removed outlier: 4.279A pdb=" N TRP Z 342 " --> pdb=" O HIS Z 338 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER Z 345 " --> pdb=" O PRO Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 355 through 369 Processing helix chain 'Z' and resid 372 through 387 removed outlier: 3.829A pdb=" N LEU Z 376 " --> pdb=" O SER Z 372 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 403 removed outlier: 4.137A pdb=" N ILE Z 394 " --> pdb=" O GLN Z 390 " (cutoff:3.500A) Processing helix chain 'Z' and resid 406 through 420 removed outlier: 3.777A pdb=" N TYR Z 410 " --> pdb=" O ARG Z 406 " (cutoff:3.500A) Processing helix chain 'Z' and resid 422 through 437 Processing helix chain 'Z' and resid 440 through 454 removed outlier: 4.014A pdb=" N GLU Z 453 " --> pdb=" O THR Z 449 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP Z 454 " --> pdb=" O VAL Z 450 " (cutoff:3.500A) Processing helix chain 'Z' and resid 457 through 472 removed outlier: 3.967A pdb=" N LYS Z 462 " --> pdb=" O GLN Z 458 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR Z 463 " --> pdb=" O GLU Z 459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 475 through 489 removed outlier: 3.626A pdb=" N GLU Z 489 " --> pdb=" O LEU Z 485 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 506 Processing sheet with id=AA1, first strand: chain 'L' and resid 22 through 24 removed outlier: 4.399A pdb=" N GLN L 155 " --> pdb=" O TYR L 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 106 through 112 removed outlier: 6.827A pdb=" N VAL L 96 " --> pdb=" O ILE L 108 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLN L 110 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE L 94 " --> pdb=" O GLN L 110 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU L 112 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER L 92 " --> pdb=" O GLU L 112 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN L 144 " --> pdb=" O PRO L 91 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS L 93 " --> pdb=" O LEU L 142 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N ARG L 133 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N ARG L 70 " --> pdb=" O ARG L 133 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE L 135 " --> pdb=" O PHE L 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.194A pdb=" N ILE A 12 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 499 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS A 508 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU A 497 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 17 through 19 removed outlier: 4.017A pdb=" N THR A 596 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP A 589 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU A 598 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE A 587 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 72 through 78 removed outlier: 6.850A pdb=" N VAL A 100 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA A 116 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP A 102 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 123 through 132 removed outlier: 4.451A pdb=" N CYS A 158 " --> pdb=" O GLN A 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 177 through 182 removed outlier: 6.709A pdb=" N GLU A 190 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 180 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 188 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N MET A 210 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 177 through 182 removed outlier: 6.709A pdb=" N GLU A 190 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 180 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 188 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N MET A 210 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 407 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 268 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR A 414 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N HIS A 266 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE A 255 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU A 249 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET A 257 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.941A pdb=" N LYS A 440 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 456 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N SER A 470 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN A 458 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE A 468 " --> pdb=" O GLN A 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 860 through 862 Processing sheet with id=AB3, first strand: chain 'A' and resid 1047 through 1048 removed outlier: 6.314A pdb=" N VAL A1047 " --> pdb=" O ARG A1110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1572 through 1574 Processing sheet with id=AB5, first strand: chain 'A' and resid 1628 through 1629 removed outlier: 3.662A pdb=" N THR A1628 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A1655 " --> pdb=" O LEU A1619 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1628 through 1629 removed outlier: 3.662A pdb=" N THR A1628 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU A1697 " --> pdb=" O LEU A1618 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A1620 " --> pdb=" O LEU A1697 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL A1699 " --> pdb=" O VAL A1620 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL A1622 " --> pdb=" O VAL A1699 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1647 through 1653 removed outlier: 3.540A pdb=" N THR A1647 " --> pdb=" O TYR A1638 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU A1635 " --> pdb=" O ILE A1666 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A1666 " --> pdb=" O GLU A1635 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR A1637 " --> pdb=" O LYS A1664 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 590 through 591 removed outlier: 6.824A pdb=" N GLY N 590 " --> pdb=" O TRP C 8 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS C 7 " --> pdb=" O THR N 645 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 635 through 637 Processing sheet with id=AC1, first strand: chain 'N' and resid 705 through 706 Processing sheet with id=AC2, first strand: chain 'I' and resid 12 through 18 removed outlier: 5.902A pdb=" N VAL I 13 " --> pdb=" O GLU I 745 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU I 745 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY I 15 " --> pdb=" O VAL I 743 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS I 740 " --> pdb=" O SER I 735 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL I 730 " --> pdb=" O GLY I 724 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLY I 724 " --> pdb=" O VAL I 730 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS I 732 " --> pdb=" O VAL I 722 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL I 722 " --> pdb=" O CYS I 732 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU I 734 " --> pdb=" O GLN I 720 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 23 through 28 removed outlier: 5.870A pdb=" N ARG I 48 " --> pdb=" O ARG I 54 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG I 54 " --> pdb=" O ARG I 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 71 through 73 removed outlier: 6.870A pdb=" N ASP I 94 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER I 100 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 112 through 117 removed outlier: 5.911A pdb=" N ILE I 185 " --> pdb=" O ARG I 197 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG I 197 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU I 187 " --> pdb=" O ILE I 195 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 204 through 210 removed outlier: 6.707A pdb=" N VAL I 220 " --> pdb=" O LEU I 206 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU I 208 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER I 218 " --> pdb=" O LEU I 208 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU I 210 " --> pdb=" O SER I 216 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N SER I 216 " --> pdb=" O LEU I 210 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER I 229 " --> pdb=" O ARG I 558 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG I 558 " --> pdb=" O SER I 229 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL I 231 " --> pdb=" O LEU I 556 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE I 552 " --> pdb=" O GLN I 235 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU I 237 " --> pdb=" O GLN I 550 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN I 550 " --> pdb=" O GLU I 237 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 574 through 578 removed outlier: 3.512A pdb=" N ILE I 590 " --> pdb=" O LYS I 597 " (cutoff:3.500A) removed outlier: 11.348A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE I 616 " --> pdb=" O ILE I 600 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE I 707 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE I 623 " --> pdb=" O PHE I 707 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 636 through 645 removed outlier: 6.746A pdb=" N VAL I 652 " --> pdb=" O LEU I 639 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA I 641 " --> pdb=" O THR I 650 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR I 650 " --> pdb=" O ALA I 641 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE I 643 " --> pdb=" O THR I 648 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR I 648 " --> pdb=" O PHE I 643 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 664 through 665 removed outlier: 4.332A pdb=" N ARG I 664 " --> pdb=" O LEU I 714 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 326 through 327 removed outlier: 3.794A pdb=" N ALA S 326 " --> pdb=" O ASP R 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 374 through 377 removed outlier: 3.779A pdb=" N SER S 374 " --> pdb=" O TYR S 387 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 193 through 195 Processing sheet with id=AD4, first strand: chain 'R' and resid 232 through 234 Processing sheet with id=AD5, first strand: chain 'R' and resid 274 through 280 removed outlier: 4.107A pdb=" N MET R 292 " --> pdb=" O SER R 288 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE R 293 " --> pdb=" O LEU R 309 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU R 309 " --> pdb=" O ILE R 293 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 320 through 321 removed outlier: 3.593A pdb=" N TYR R 351 " --> pdb=" O LEU R 337 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN R 349 " --> pdb=" O VAL R 339 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 361 through 363 removed outlier: 3.599A pdb=" N ALA R 362 " --> pdb=" O ALA R 372 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE R 382 " --> pdb=" O CYS R 395 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS R 395 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE R 384 " --> pdb=" O LEU R 393 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 402 through 406 removed outlier: 3.776A pdb=" N ASN R 404 " --> pdb=" O THR R 417 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN R 424 " --> pdb=" O HIS R 418 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA R 437 " --> pdb=" O VAL R 427 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 46 through 48 4247 hydrogen bonds defined for protein. 12511 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: 26.37 Time building geometry restraints manager: 14.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 21744 1.34 - 1.46: 15163 1.46 - 1.58: 30555 1.58 - 1.70: 0 1.70 - 1.82: 589 Bond restraints: 68051 Sorted by residual: bond pdb=" N PHE S 403 " pdb=" CA PHE S 403 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N ILE R 458 " pdb=" CA ILE R 458 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.64e+00 bond pdb=" N VAL R 459 " pdb=" CA VAL R 459 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 9.05e+00 bond pdb=" N TYR R 420 " pdb=" CA TYR R 420 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.81e+00 bond pdb=" N ILE I 600 " pdb=" CA ILE I 600 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.70e+00 ... (remaining 68046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 91529 2.91 - 5.83: 750 5.83 - 8.74: 72 8.74 - 11.66: 22 11.66 - 14.57: 10 Bond angle restraints: 92383 Sorted by residual: angle pdb=" C MET A1652 " pdb=" N ALA A1653 " pdb=" CA ALA A1653 " ideal model delta sigma weight residual 120.68 129.02 -8.34 1.52e+00 4.33e-01 3.01e+01 angle pdb=" C GLU A1284 " pdb=" CA GLU A1284 " pdb=" CB GLU A1284 " ideal model delta sigma weight residual 116.54 110.57 5.97 1.15e+00 7.56e-01 2.69e+01 angle pdb=" CB MET V 229 " pdb=" CG MET V 229 " pdb=" SD MET V 229 " ideal model delta sigma weight residual 112.70 98.13 14.57 3.00e+00 1.11e-01 2.36e+01 angle pdb=" CB MET Y 224 " pdb=" CG MET Y 224 " pdb=" SD MET Y 224 " ideal model delta sigma weight residual 112.70 127.26 -14.56 3.00e+00 1.11e-01 2.35e+01 angle pdb=" CA PRO R 182 " pdb=" C PRO R 182 " pdb=" O PRO R 182 " ideal model delta sigma weight residual 121.31 117.76 3.55 7.40e-01 1.83e+00 2.30e+01 ... (remaining 92378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 36420 18.05 - 36.09: 3493 36.09 - 54.14: 682 54.14 - 72.18: 169 72.18 - 90.23: 53 Dihedral angle restraints: 40817 sinusoidal: 15468 harmonic: 25349 Sorted by residual: dihedral pdb=" CA PHE N 162 " pdb=" C PHE N 162 " pdb=" N PHE N 163 " pdb=" CA PHE N 163 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY N 510 " pdb=" C GLY N 510 " pdb=" N SER N 511 " pdb=" CA SER N 511 " ideal model delta harmonic sigma weight residual -180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA VAL O 369 " pdb=" C VAL O 369 " pdb=" N HIS O 370 " pdb=" CA HIS O 370 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 40814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 8582 0.053 - 0.106: 1663 0.106 - 0.159: 226 0.159 - 0.212: 34 0.212 - 0.265: 3 Chirality restraints: 10508 Sorted by residual: chirality pdb=" CG LEU D 41 " pdb=" CB LEU D 41 " pdb=" CD1 LEU D 41 " pdb=" CD2 LEU D 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ILE D 44 " pdb=" N ILE D 44 " pdb=" C ILE D 44 " pdb=" CB ILE D 44 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA VAL Z 310 " pdb=" N VAL Z 310 " pdb=" C VAL Z 310 " pdb=" CB VAL Z 310 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 10505 not shown) Planarity restraints: 11784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1803 " 0.270 9.50e-02 1.11e+02 1.21e-01 8.98e+00 pdb=" NE ARG A1803 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A1803 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1803 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1803 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG U 310 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C ARG U 310 " -0.049 2.00e-02 2.50e+03 pdb=" O ARG U 310 " 0.018 2.00e-02 2.50e+03 pdb=" N SER U 311 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1802 " 0.244 9.50e-02 1.11e+02 1.10e-01 7.36e+00 pdb=" NE ARG A1802 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A1802 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1802 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1802 " 0.008 2.00e-02 2.50e+03 ... (remaining 11781 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5883 2.74 - 3.28: 70517 3.28 - 3.82: 118348 3.82 - 4.36: 135539 4.36 - 4.90: 231343 Nonbonded interactions: 561630 Sorted by model distance: nonbonded pdb=" O PRO A1096 " pdb=" NE2 GLN O 332 " model vdw 2.198 3.120 nonbonded pdb=" OH TYR J 73 " pdb=" O HIS P 18 " model vdw 2.205 3.040 nonbonded pdb=" N GLU H 90 " pdb=" OE1 GLU H 90 " model vdw 2.208 3.120 nonbonded pdb=" OD1 ASP I 645 " pdb=" OG1 THR I 648 " model vdw 2.209 3.040 nonbonded pdb=" N GLU G 17 " pdb=" OE1 GLU G 17 " model vdw 2.209 3.120 ... (remaining 561625 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 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 1 through 24 or (resid 25 through 26 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'W' and (resid 1 through 23 or (resid 24 through 26 and (name N or name C \ A or name C or name O or name CB )))) } ncs_group { reference = (chain 'J' and (resid 5 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 615 or (resid 616 and (name N or \ name CA or name C or name O or name CB )) or resid 617 through 744 or (resid 74 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 746 through \ 769)) selection = (chain 'P' and (resid 5 through 97 or (resid 98 through 99 and (name N or name C \ A or name C or name O or name CB )) or resid 100 or (resid 101 and (name N or na \ me CA or name C or name O or name CB )) or resid 102 through 170 or (resid 171 a \ nd (name N or name CA or name C or name O or name CB )) or resid 451 through 454 \ or (resid 455 and (name N or name CA or name C or name O or name CB )) or resid \ 456 through 459 or (resid 460 and (name N or name CA or name C or name O or nam \ e CB )) or resid 461 through 654 or (resid 655 and (name N or name CA or name C \ or name O or name CB )) or resid 656 through 685 or (resid 686 through 688 and ( \ name N or name CA or name C or name O or name CB )) or resid 689 through 726 or \ (resid 727 and (name N or name CA or name C or name O or name CB )) or resid 728 \ through 748 or (resid 749 and (name N or name CA or name C or name O or name CB \ )) or resid 750 through 769)) } ncs_group { reference = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 216 or (resid 217 and (name N or name CA or name C or name \ O or name CB )) or resid 218 or (resid 219 through 223 and (name N or name CA or \ name C or name O or name CB )) or resid 224 or (resid 225 and (name N or name C \ A or name C or name O or name CB )) or resid 226 through 316 or (resid 317 and ( \ name N or name CA or name C or name O or name CB )) or resid 318 through 495 or \ (resid 496 and (name N or name CA or name C or name O or name CB )) or resid 497 \ through 509 or resid 511 through 528 or resid 548 or resid 560)) selection = (chain 'Q' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 124 or resid 128 through 388 or (resid \ 389 and (name N or name CA or name C or name O or name CB )) or resid 390 throu \ gh 436 or (resid 437 through 438 and (name N or name CA or name C or name O or n \ ame CB )) or resid 439 through 509 or resid 511 through 530)) } ncs_group { reference = (chain 'U' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 43 or resid 45 through 164 or (resid 165 and (name N or n \ ame CA or name C or name O or name CB )) or resid 166 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 25 \ 5 or (resid 256 and (name N or name CA or name C or name O or name CB )) or resi \ d 257 through 280 or (resid 281 through 282 and (name N or name CA or name C or \ name O or name CB )) or resid 283 through 477 or (resid 478 through 479 and (nam \ e N or name CA or name C or name O or name CB )) or resid 480 through 496 or (re \ sid 497 through 498 and (name N or name CA or name C or name O or name CB )) or \ resid 499 through 502 or resid 510 through 520 or (resid 521 through 523 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'V' and (resid 25 through 43 or resid 45 through 133 or (resid 134 and (n \ ame N or name CA or name C or name O or name CB )) or resid 135 or resid 147 thr \ ough 185 or (resid 186 and (name N or name CA or name C or name O or name CB )) \ or resid 187 through 193 or (resid 194 through 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 through 412 or (resid 413 and (name N o \ r name CA or name C or name O or name CB )) or resid 414 through 432 or (resid 4 \ 33 and (name N or name CA or name C or name O or name CB )) or resid 434 through \ 452 or (resid 453 and (name N or name CA or name C or name O or name CB )) or r \ esid 454 through 456 or (resid 457 and (name N or name CA or name C or name O or \ name CB )) or resid 458 through 466 or (resid 467 through 469 and (name N or na \ me CA or name C or name O or name CB )) or resid 470 through 471 or (resid 472 a \ nd (name N or name CA or name C or name O or name CB )) or resid 473 through 475 \ or (resid 476 and (name N or name CA or name C or name O or name CB )) or resid \ 477 through 478 or (resid 479 and (name N or name CA or name C or name O or nam \ e CB )) or resid 480 through 483 or (resid 484 through 489 and (name N or name C \ A or name C or name O or name CB )) or resid 490 or (resid 491 and (name N or na \ me CA or name C or name O or name CB )) or resid 492 through 497 or (resid 498 a \ nd (name N or name CA or name C or name O or name CB )) or resid 499 through 510 \ or (resid 511 through 514 and (name N or name CA or name C or name O or name CB \ )) or resid 515 or (resid 516 through 523 and (name N or name CA or name C or n \ ame O or name CB )))) } ncs_group { reference = (chain 'Y' and (resid 35 through 88 or (resid 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 149 or (resid 150 and (name N or n \ ame CA or name C or name O or name CB )) or resid 151 through 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB )) or resid 216 through 22 \ 1 or (resid 222 and (name N or name CA or name C or name O or name CB )) or resi \ d 223 or (resid 224 through 225 and (name N or name CA or name C or name O or na \ me CB )) or resid 226 through 227 or (resid 228 and (name N or name CA or name C \ or name O or name CB )) or resid 229 through 235 or (resid 236 and (name N or n \ ame CA or name C or name O or name CB )) or resid 237 through 240 or (resid 241 \ through 242 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 3 through 260 or (resid 261 through 265 and (name N or name CA or name C or name \ O or name CB )) or resid 266 through 267 or (resid 268 and (name N or name CA o \ r name C or name O or name CB )) or resid 269 through 276 or (resid 277 through \ 278 and (name N or name CA or name C or name O or name CB )) or resid 279 throug \ h 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or \ resid 282 through 294 or (resid 295 and (name N or name CA or name C or name O o \ r name CB )) or resid 296 through 326 or (resid 327 and (name N or name CA or na \ me C or name O or name CB )) or resid 328 through 333 or (resid 334 and (name N \ or name CA or name C or name O or name CB )) or resid 335 through 336 or (resid \ 337 and (name N or name CA or name C or name O or name CB )) or resid 338 throug \ h 376 or (resid 377 and (name N or name CA or name C or name O or name CB )) or \ resid 378 or (resid 379 and (name N or name CA or name C or name O or name CB )) \ or resid 380 through 389 or (resid 390 through 392 and (name N or name CA or na \ me C or name O or name CB )) or resid 393 through 420 or (resid 421 and (name N \ or name CA or name C or name O or name CB )) or resid 422 or (resid 423 through \ 427 and (name N or name CA or name C or name O or name CB )) or resid 428 throug \ h 431 or (resid 432 and (name N or name CA or name C or name O or name CB )) or \ resid 433 through 445 or (resid 446 and (name N or name CA or name C or name O o \ r name CB )) or resid 447 through 449 or (resid 450 and (name N or name CA or na \ me C or name O or name CB )) or resid 451 through 454 or (resid 455 through 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 or (resid \ 464 and (name N or name CA or name C or name O or name CB )) or resid 465 or (re \ sid 466 through 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 470 or (resid 471 through 478 and (name N or name CA or name C \ or name O or name CB )) or resid 479 through 481 or (resid 482 through 486 and \ (name N or name CA or name C or name O or name CB )) or resid 487 or (resid 488 \ through 494 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 5 or (resid 496 through 499 and (name N or name CA or name C or name O or name C \ B )) or (resid 501 through 507 and (name N or name CA or name C or name O or nam \ e CB )))) selection = (chain 'Z' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 62 or (resid 63 and (name N or name CA or name C or name \ O or name CB )) or resid 64 through 106 or (resid 107 through 110 and (name N or \ name CA or name C or name O or name CB )) or resid 132 through 136 or (resid 13 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 138 or (resi \ d 139 and (name N or name CA or name C or name O or name CB )) or resid 140 or ( \ resid 141 and (name N or name CA or name C or name O or name CB )) or resid 142 \ through 145 or (resid 146 and (name N or name CA or name C or name O or name CB \ )) or resid 147 through 152 or (resid 153 and (name N or name CA or name C or na \ me O or name CB )) or resid 154 through 166 or (resid 167 and (name N or name CA \ or name C or name O or name CB )) or resid 168 through 172 or (resid 173 and (n \ ame N or name CA or name C or name O or name CB )) or resid 174 or (resid 175 th \ rough 176 and (name N or name CA or name C or name O or name CB )) or resid 177 \ through 249 or (resid 250 and (name N or name CA or name C or name O or name CB \ )) or resid 251 through 282 or (resid 283 through 284 and (name N or name CA or \ name C or name O or name CB )) or resid 285 through 287 or (resid 288 and (name \ N or name CA or name C or name O or name CB )) or resid 289 through 305 or (resi \ d 306 and (name N or name CA or name C or name O or name CB )) or resid 307 thro \ ugh 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) o \ r resid 319 through 396 or (resid 397 through 399 and (name N or name CA or name \ C or name O or name CB )) or resid 400 through 407 or (resid 408 and (name N or \ name CA or name C or name O or name CB )) or resid 409 through 414 or (resid 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 and (name N or name CA or name C or name O or name CB )) or resid 418 thro \ ugh 428 or (resid 429 through 430 and (name N or name CA or name C or name O or \ name CB )) or resid 431 through 499 or resid 501 through 507)) } 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=0.14 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.090 Extract box with map and model: 1.960 Check model and map are aligned: 0.370 Set scattering table: 0.480 Process input model: 125.260 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.270 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:8.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 : 0.004 0.089 68051 Z= 0.258 Angle : 0.699 14.572 92383 Z= 0.407 Chirality : 0.042 0.265 10508 Planarity : 0.004 0.121 11784 Dihedral : 15.057 90.228 24379 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 0.78 % Allowed : 16.56 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.09), residues: 8472 helix: 1.77 (0.07), residues: 5524 sheet: -0.37 (0.22), residues: 549 loop : -1.14 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP Y 239 HIS 0.007 0.001 HIS U 321 PHE 0.021 0.001 PHE Z 332 TYR 0.028 0.001 TYR S 387 ARG 0.016 0.001 ARG Y 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 423 time to evaluate : 5.725 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: N 563 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7137 (t0) outliers start: 54 outliers final: 38 residues processed: 472 average time/residue: 1.4707 time to fit residues: 907.0528 Evaluate side-chains 399 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 360 time to evaluate : 5.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain N residue 563 ASP Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain O residue 11 ASN Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain S residue 406 CYS Chi-restraints excluded: chain S residue 409 CYS Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain J residue 612 VAL Chi-restraints excluded: chain P residue 115 CYS Chi-restraints excluded: chain Q residue 175 MET Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 233 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain Z residue 267 LEU Chi-restraints excluded: chain Z residue 344 VAL Chi-restraints excluded: chain Z residue 480 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 716 optimal weight: 0.9980 chunk 643 optimal weight: 4.9990 chunk 357 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 434 optimal weight: 0.9990 chunk 343 optimal weight: 5.9990 chunk 665 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 404 optimal weight: 9.9990 chunk 495 optimal weight: 6.9990 chunk 770 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 160 ASN A 592 HIS A1602 HIS A1869 HIS ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 GLN ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 472 HIS ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 659 GLN Y 36 ASN Y 83 HIS Y 106 GLN ** Y 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS V 477 HIS R 65 ASN R 158 GLN R 401 GLN R 423 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 ASN ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 296 GLN Z 338 HIS Z 395 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 68051 Z= 0.200 Angle : 0.563 11.849 92383 Z= 0.285 Chirality : 0.039 0.204 10508 Planarity : 0.004 0.048 11784 Dihedral : 4.350 59.000 9343 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 1.74 % Allowed : 16.04 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.09), residues: 8472 helix: 1.88 (0.07), residues: 5548 sheet: -0.26 (0.22), residues: 537 loop : -1.03 (0.13), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 239 HIS 0.007 0.001 HIS U 321 PHE 0.032 0.001 PHE Q 164 TYR 0.024 0.001 TYR S 413 ARG 0.012 0.000 ARG Q 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 393 time to evaluate : 5.857 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: D 36 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7722 (tm-30) REVERT: H 87 GLU cc_start: 0.7138 (pm20) cc_final: 0.6931 (pm20) REVERT: P 764 MET cc_start: 0.8449 (mmt) cc_final: 0.8219 (mmm) REVERT: R 1 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6971 (ttt) REVERT: R 328 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7838 (pp) REVERT: R 418 HIS cc_start: 0.8575 (m-70) cc_final: 0.8079 (m-70) outliers start: 120 outliers final: 36 residues processed: 486 average time/residue: 1.3854 time to fit residues: 900.3067 Evaluate side-chains 396 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 358 time to evaluate : 5.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1378 THR Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain N residue 137 ARG Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 555 HIS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 448 MET Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain Y residue 409 CYS Chi-restraints excluded: chain U residue 442 CYS Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 328 LEU Chi-restraints excluded: chain R residue 488 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain Z residue 219 VAL Chi-restraints excluded: chain Z residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 428 optimal weight: 0.9980 chunk 239 optimal weight: 20.0000 chunk 641 optimal weight: 9.9990 chunk 524 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 772 optimal weight: 0.0060 chunk 834 optimal weight: 20.0000 chunk 687 optimal weight: 9.9990 chunk 765 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 619 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 676 ASN I 684 GLN ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 228 GLN ** Y 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS C 78 GLN ** Z 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68051 Z= 0.206 Angle : 0.550 11.131 92383 Z= 0.276 Chirality : 0.038 0.218 10508 Planarity : 0.003 0.049 11784 Dihedral : 4.079 58.422 9308 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.99 % Favored : 96.99 % Rotamer: Outliers : 1.97 % Allowed : 16.56 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.09), residues: 8472 helix: 1.96 (0.07), residues: 5540 sheet: -0.22 (0.22), residues: 537 loop : -0.98 (0.13), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP Y 239 HIS 0.007 0.001 HIS U 321 PHE 0.042 0.001 PHE Q 164 TYR 0.023 0.001 TYR Z 93 ARG 0.009 0.000 ARG G 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 382 time to evaluate : 5.804 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: D 36 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7599 (tm-30) REVERT: D 51 LEU cc_start: 0.8548 (tp) cc_final: 0.8344 (tt) REVERT: N 560 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8724 (tpp) REVERT: I 705 MET cc_start: 0.7907 (mmm) cc_final: 0.7609 (mmt) REVERT: H 85 LEU cc_start: 0.8171 (tp) cc_final: 0.7887 (tm) REVERT: P 764 MET cc_start: 0.8462 (mmt) cc_final: 0.8239 (mmm) REVERT: R 418 HIS cc_start: 0.8618 (m-70) cc_final: 0.8417 (m-70) outliers start: 136 outliers final: 45 residues processed: 487 average time/residue: 1.3659 time to fit residues: 888.2859 Evaluate side-chains 405 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 359 time to evaluate : 5.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 173 CYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1378 THR Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain N residue 137 ARG Chi-restraints excluded: chain N residue 555 HIS Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 686 THR Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 448 MET Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 687 LEU Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain Y residue 92 GLU Chi-restraints excluded: chain Y residue 409 CYS Chi-restraints excluded: chain U residue 414 MET Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 488 VAL Chi-restraints excluded: chain C residue 17 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 763 optimal weight: 0.9980 chunk 580 optimal weight: 1.9990 chunk 400 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 368 optimal weight: 0.9990 chunk 518 optimal weight: 1.9990 chunk 775 optimal weight: 9.9990 chunk 820 optimal weight: 6.9990 chunk 404 optimal weight: 9.9990 chunk 734 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A1165 HIS N 239 GLN ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 ASN ** J 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN V 202 HIS R 185 GLN R 394 GLN R 471 ASN ** Z 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 68051 Z= 0.193 Angle : 0.546 12.264 92383 Z= 0.274 Chirality : 0.038 0.317 10508 Planarity : 0.003 0.044 11784 Dihedral : 4.026 55.828 9304 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 2.02 % Allowed : 17.06 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 8472 helix: 2.02 (0.07), residues: 5539 sheet: -0.13 (0.22), residues: 537 loop : -0.94 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP Y 239 HIS 0.007 0.001 HIS U 321 PHE 0.046 0.001 PHE Q 164 TYR 0.023 0.001 TYR S 387 ARG 0.010 0.000 ARG V 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 379 time to evaluate : 5.759 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: D 36 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7558 (tm-30) REVERT: N 560 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8709 (tpp) REVERT: I 705 MET cc_start: 0.7944 (mmm) cc_final: 0.7539 (mmt) REVERT: W 1 MET cc_start: 0.7835 (tpp) cc_final: 0.7607 (tpp) REVERT: P 764 MET cc_start: 0.8536 (mmt) cc_final: 0.8329 (mmm) REVERT: U 414 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6934 (mtt) REVERT: R 418 HIS cc_start: 0.8627 (m-70) cc_final: 0.8090 (m-70) outliers start: 140 outliers final: 56 residues processed: 490 average time/residue: 1.3384 time to fit residues: 882.7659 Evaluate side-chains 414 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 356 time to evaluate : 5.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 173 CYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1378 THR Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain N residue 137 ARG Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 555 HIS Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 686 THR Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 448 MET Chi-restraints excluded: chain O residue 624 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 687 LEU Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain J residue 596 VAL Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain Y residue 92 GLU Chi-restraints excluded: chain Y residue 409 CYS Chi-restraints excluded: chain U residue 414 MET Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 488 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain Z residue 219 VAL Chi-restraints excluded: chain Z residue 267 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 683 optimal weight: 7.9990 chunk 465 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 611 optimal weight: 20.0000 chunk 338 optimal weight: 8.9990 chunk 700 optimal weight: 1.9990 chunk 567 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 419 optimal weight: 2.9990 chunk 736 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 HIS ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 414 HIS ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS R 185 GLN ** Z 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 68051 Z= 0.318 Angle : 0.597 10.399 92383 Z= 0.300 Chirality : 0.040 0.227 10508 Planarity : 0.004 0.057 11784 Dihedral : 4.041 55.154 9301 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.84 % Rotamer: Outliers : 1.88 % Allowed : 17.54 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.09), residues: 8472 helix: 2.03 (0.07), residues: 5571 sheet: -0.18 (0.22), residues: 560 loop : -0.89 (0.13), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP Y 239 HIS 0.007 0.001 HIS U 321 PHE 0.047 0.001 PHE Q 164 TYR 0.027 0.001 TYR S 405 ARG 0.011 0.000 ARG L 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 368 time to evaluate : 6.795 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: D 36 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 1078 MET cc_start: 0.8530 (mtp) cc_final: 0.8211 (mtm) REVERT: N 560 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8646 (tpp) REVERT: I 705 MET cc_start: 0.7946 (mmm) cc_final: 0.7503 (mmt) REVERT: P 764 MET cc_start: 0.8544 (mmt) cc_final: 0.8340 (mmm) REVERT: U 414 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.6997 (mtt) REVERT: R 1 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7098 (ttt) REVERT: R 418 HIS cc_start: 0.8639 (m-70) cc_final: 0.8115 (m-70) outliers start: 130 outliers final: 66 residues processed: 467 average time/residue: 1.3695 time to fit residues: 854.4371 Evaluate side-chains 420 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 351 time to evaluate : 5.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 173 CYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain N residue 137 ARG Chi-restraints excluded: chain N residue 353 ASP Chi-restraints excluded: chain N residue 555 HIS Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 686 THR Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 448 MET Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 624 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 687 LEU Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain J residue 596 VAL Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 612 VAL Chi-restraints excluded: chain Y residue 409 CYS Chi-restraints excluded: chain U residue 414 MET Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 488 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain Z residue 199 CYS Chi-restraints excluded: chain Z residue 219 VAL Chi-restraints excluded: chain Z residue 267 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 276 optimal weight: 5.9990 chunk 739 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 481 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 821 optimal weight: 0.0570 chunk 681 optimal weight: 0.9990 chunk 380 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 431 optimal weight: 2.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 186 GLN ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN ** J 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 162 HIS V 202 HIS R 185 GLN ** Z 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 68051 Z= 0.169 Angle : 0.560 12.675 92383 Z= 0.277 Chirality : 0.038 0.223 10508 Planarity : 0.003 0.044 11784 Dihedral : 4.009 53.835 9301 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.91 % Favored : 97.08 % Rotamer: Outliers : 1.71 % Allowed : 18.03 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.09), residues: 8472 helix: 2.05 (0.07), residues: 5556 sheet: -0.19 (0.22), residues: 554 loop : -0.87 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Y 239 HIS 0.007 0.001 HIS S 414 PHE 0.048 0.001 PHE Q 164 TYR 0.031 0.001 TYR S 405 ARG 0.010 0.000 ARG L 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 384 time to evaluate : 5.917 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: D 36 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 1078 MET cc_start: 0.8502 (mtp) cc_final: 0.8200 (mtm) REVERT: N 560 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8715 (tpp) REVERT: I 705 MET cc_start: 0.7906 (mmm) cc_final: 0.7469 (mmt) REVERT: P 764 MET cc_start: 0.8568 (mmt) cc_final: 0.8361 (mmm) REVERT: U 414 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6954 (mtt) REVERT: R 266 MET cc_start: 0.5293 (OUTLIER) cc_final: 0.4825 (tpp) REVERT: Z 429 MET cc_start: 0.8275 (ppp) cc_final: 0.8069 (ppp) outliers start: 118 outliers final: 56 residues processed: 480 average time/residue: 1.3668 time to fit residues: 876.0951 Evaluate side-chains 416 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 357 time to evaluate : 5.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 934 MET Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1378 THR Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain N residue 137 ARG Chi-restraints excluded: chain N residue 555 HIS Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 624 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 687 LEU Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain J residue 596 VAL Chi-restraints excluded: chain J residue 612 VAL Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain Y residue 92 GLU Chi-restraints excluded: chain Y residue 409 CYS Chi-restraints excluded: chain U residue 210 CYS Chi-restraints excluded: chain U residue 414 MET Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 487 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain Z residue 199 CYS Chi-restraints excluded: chain Z residue 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 791 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 468 optimal weight: 6.9990 chunk 599 optimal weight: 2.9990 chunk 464 optimal weight: 8.9990 chunk 691 optimal weight: 10.0000 chunk 458 optimal weight: 7.9990 chunk 818 optimal weight: 9.9990 chunk 512 optimal weight: 7.9990 chunk 498 optimal weight: 7.9990 chunk 377 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN A 832 HIS A1075 GLN A1486 ASN ** N 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 ASN I 668 GLN ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 556 GLN ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN ** J 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 GLN ** Z 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 68051 Z= 0.459 Angle : 0.686 15.035 92383 Z= 0.342 Chirality : 0.042 0.264 10508 Planarity : 0.004 0.076 11784 Dihedral : 4.167 54.737 9301 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.59 % Favored : 96.40 % Rotamer: Outliers : 1.92 % Allowed : 18.44 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.09), residues: 8472 helix: 1.98 (0.07), residues: 5559 sheet: -0.26 (0.22), residues: 574 loop : -0.90 (0.13), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Y 239 HIS 0.007 0.001 HIS U 321 PHE 0.048 0.002 PHE Q 164 TYR 0.035 0.002 TYR S 405 ARG 0.011 0.001 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 366 time to evaluate : 5.777 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: D 36 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 1078 MET cc_start: 0.8586 (mtp) cc_final: 0.8375 (mtm) REVERT: A 1285 MET cc_start: 0.7423 (mpm) cc_final: 0.7215 (mpm) REVERT: N 560 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8646 (tpp) REVERT: I 440 MET cc_start: 0.7669 (mmt) cc_final: 0.7428 (mpp) REVERT: I 705 MET cc_start: 0.7944 (mmm) cc_final: 0.7510 (mmt) REVERT: P 764 MET cc_start: 0.8576 (mmt) cc_final: 0.8372 (mmm) REVERT: U 414 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7009 (mtt) REVERT: R 1 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7039 (ttt) REVERT: R 266 MET cc_start: 0.5455 (OUTLIER) cc_final: 0.5161 (tpp) outliers start: 133 outliers final: 67 residues processed: 476 average time/residue: 1.3610 time to fit residues: 869.4859 Evaluate side-chains 419 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 348 time to evaluate : 5.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 173 CYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain N residue 137 ARG Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain N residue 555 HIS Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 686 THR Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 426 THR Chi-restraints excluded: chain O residue 448 MET Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 624 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 687 LEU Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 596 VAL Chi-restraints excluded: chain J residue 612 VAL Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 612 VAL Chi-restraints excluded: chain Y residue 409 CYS Chi-restraints excluded: chain Y residue 546 LEU Chi-restraints excluded: chain U residue 414 MET Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 487 SER Chi-restraints excluded: chain R residue 488 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain Z residue 199 CYS Chi-restraints excluded: chain Z residue 267 LEU Chi-restraints excluded: chain Z residue 347 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 506 optimal weight: 0.8980 chunk 326 optimal weight: 0.9990 chunk 488 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 520 optimal weight: 4.9990 chunk 557 optimal weight: 5.9990 chunk 404 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 643 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN J 657 HIS ** J 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 GLN Z 52 ASN ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 68051 Z= 0.219 Angle : 0.610 14.067 92383 Z= 0.300 Chirality : 0.039 0.301 10508 Planarity : 0.003 0.059 11784 Dihedral : 4.127 53.714 9301 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.06 % Favored : 96.93 % Rotamer: Outliers : 1.39 % Allowed : 19.29 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.09), residues: 8472 helix: 2.03 (0.07), residues: 5560 sheet: -0.38 (0.22), residues: 570 loop : -0.84 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Y 239 HIS 0.008 0.001 HIS U 321 PHE 0.051 0.001 PHE Q 164 TYR 0.037 0.001 TYR S 405 ARG 0.013 0.000 ARG J 629 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 366 time to evaluate : 5.779 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: D 36 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 1078 MET cc_start: 0.8495 (mtp) cc_final: 0.8270 (mtm) REVERT: N 560 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8606 (tpp) REVERT: I 440 MET cc_start: 0.7756 (mmt) cc_final: 0.7271 (mpp) REVERT: I 705 MET cc_start: 0.7958 (mmm) cc_final: 0.7547 (mmt) REVERT: M 53 GLN cc_start: 0.7344 (pt0) cc_final: 0.6885 (pt0) REVERT: U 414 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7007 (mtt) outliers start: 96 outliers final: 62 residues processed: 443 average time/residue: 1.4016 time to fit residues: 840.5176 Evaluate side-chains 415 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 351 time to evaluate : 6.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 934 MET Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain N residue 555 HIS Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 686 THR Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 624 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 687 LEU Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain S residue 406 CYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 596 VAL Chi-restraints excluded: chain J residue 612 VAL Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain Q residue 185 LEU Chi-restraints excluded: chain Y residue 92 GLU Chi-restraints excluded: chain Y residue 409 CYS Chi-restraints excluded: chain Y residue 546 LEU Chi-restraints excluded: chain U residue 414 MET Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 487 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain Z residue 199 CYS Chi-restraints excluded: chain Z residue 267 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 744 optimal weight: 5.9990 chunk 783 optimal weight: 20.0000 chunk 715 optimal weight: 1.9990 chunk 762 optimal weight: 0.0770 chunk 458 optimal weight: 6.9990 chunk 332 optimal weight: 9.9990 chunk 598 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 689 optimal weight: 5.9990 chunk 721 optimal weight: 2.9990 chunk 759 optimal weight: 0.0670 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 68051 Z= 0.180 Angle : 0.615 16.059 92383 Z= 0.300 Chirality : 0.038 0.301 10508 Planarity : 0.003 0.045 11784 Dihedral : 4.067 51.289 9301 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.09 % Favored : 96.89 % Rotamer: Outliers : 1.20 % Allowed : 19.46 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.09), residues: 8472 helix: 2.05 (0.07), residues: 5553 sheet: -0.27 (0.22), residues: 561 loop : -0.82 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP Y 239 HIS 0.007 0.001 HIS U 321 PHE 0.049 0.001 PHE Q 164 TYR 0.037 0.001 TYR S 405 ARG 0.008 0.000 ARG M 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 374 time to evaluate : 5.945 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: D 36 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 1078 MET cc_start: 0.8505 (mtp) cc_final: 0.8248 (mtm) REVERT: I 705 MET cc_start: 0.7974 (mmm) cc_final: 0.7557 (mmt) REVERT: G 23 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7714 (mmm160) REVERT: U 218 MET cc_start: 0.7910 (pmm) cc_final: 0.7378 (ptp) REVERT: U 414 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6964 (mtt) REVERT: R 266 MET cc_start: 0.5367 (tpp) cc_final: 0.4617 (tpp) REVERT: R 418 HIS cc_start: 0.8522 (m-70) cc_final: 0.8264 (m-70) REVERT: C 19 ASN cc_start: 0.6532 (p0) cc_final: 0.6278 (p0) outliers start: 83 outliers final: 61 residues processed: 439 average time/residue: 1.3883 time to fit residues: 814.7176 Evaluate side-chains 414 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 352 time to evaluate : 5.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain N residue 555 HIS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 686 THR Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 250 PHE Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 624 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 687 LEU Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain S residue 405 TYR Chi-restraints excluded: chain S residue 406 CYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain J residue 596 VAL Chi-restraints excluded: chain J residue 612 VAL Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 612 VAL Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain Q residue 185 LEU Chi-restraints excluded: chain Y residue 92 GLU Chi-restraints excluded: chain Y residue 409 CYS Chi-restraints excluded: chain U residue 414 MET Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 487 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain Z residue 199 CYS Chi-restraints excluded: chain Z residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 500 optimal weight: 5.9990 chunk 806 optimal weight: 5.9990 chunk 492 optimal weight: 0.9990 chunk 382 optimal weight: 5.9990 chunk 560 optimal weight: 7.9990 chunk 845 optimal weight: 50.0000 chunk 778 optimal weight: 8.9990 chunk 673 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 520 optimal weight: 4.9990 chunk 412 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1555 HIS ** N 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 241 HIS ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 68051 Z= 0.325 Angle : 0.652 17.269 92383 Z= 0.321 Chirality : 0.040 0.278 10508 Planarity : 0.004 0.064 11784 Dihedral : 4.101 51.570 9301 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.26 % Favored : 96.73 % Rotamer: Outliers : 1.13 % Allowed : 19.51 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.09), residues: 8472 helix: 2.07 (0.07), residues: 5553 sheet: -0.25 (0.22), residues: 570 loop : -0.83 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP Y 239 HIS 0.007 0.001 HIS U 321 PHE 0.053 0.001 PHE Q 164 TYR 0.037 0.001 TYR S 405 ARG 0.017 0.000 ARG J 629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16944 Ramachandran restraints generated. 8472 Oldfield, 0 Emsley, 8472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 359 time to evaluate : 5.899 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: D 36 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 1078 MET cc_start: 0.8566 (mtp) cc_final: 0.8341 (mtm) REVERT: A 1731 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7666 (mmp-170) REVERT: I 705 MET cc_start: 0.8021 (mmm) cc_final: 0.7593 (mmt) REVERT: P 764 MET cc_start: 0.8563 (mmt) cc_final: 0.8334 (mmm) REVERT: U 218 MET cc_start: 0.8023 (pmm) cc_final: 0.7493 (ptp) REVERT: U 414 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6983 (mtt) REVERT: R 418 HIS cc_start: 0.8545 (m-70) cc_final: 0.8266 (m-70) REVERT: C 19 ASN cc_start: 0.6536 (p0) cc_final: 0.6240 (p0) REVERT: Z 429 MET cc_start: 0.8110 (ppp) cc_final: 0.7834 (ppp) outliers start: 78 outliers final: 61 residues processed: 423 average time/residue: 1.3739 time to fit residues: 779.9638 Evaluate side-chains 412 residues out of total 7546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 350 time to evaluate : 5.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain N residue 555 HIS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 686 THR Chi-restraints excluded: chain I residue 700 ILE Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 458 VAL Chi-restraints excluded: chain O residue 574 LEU Chi-restraints excluded: chain O residue 624 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 687 LEU Chi-restraints excluded: chain S residue 323 THR Chi-restraints excluded: chain S residue 405 TYR Chi-restraints excluded: chain S residue 406 CYS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 354 MET Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain J residue 596 VAL Chi-restraints excluded: chain J residue 612 VAL Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 643 MET Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 612 VAL Chi-restraints excluded: chain Q residue 185 LEU Chi-restraints excluded: chain Y residue 409 CYS Chi-restraints excluded: chain Y residue 546 LEU Chi-restraints excluded: chain U residue 414 MET Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 487 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain Z residue 199 CYS Chi-restraints excluded: chain Z residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 534 optimal weight: 0.7980 chunk 717 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 621 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 674 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 chunk 692 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.048932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.036307 restraints weight = 373055.913| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.61 r_work: 0.2772 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 68051 Z= 0.280 Angle : 0.652 16.555 92383 Z= 0.320 Chirality : 0.040 0.274 10508 Planarity : 0.003 0.050 11784 Dihedral : 4.128 52.090 9301 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 1.08 % Allowed : 19.70 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.09), residues: 8472 helix: 2.04 (0.07), residues: 5556 sheet: -0.22 (0.22), residues: 565 loop : -0.81 (0.13), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP Y 239 HIS 0.007 0.001 HIS U 321 PHE 0.053 0.001 PHE Q 164 TYR 0.040 0.001 TYR S 405 ARG 0.009 0.000 ARG M 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15985.66 seconds wall clock time: 281 minutes 15.01 seconds (16875.01 seconds total)