Starting phenix.real_space_refine (version: dev) on Mon Dec 19 16:48:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9g_27963/12_2022/8e9g_27963_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9g_27963/12_2022/8e9g_27963.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9g_27963/12_2022/8e9g_27963_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9g_27963/12_2022/8e9g_27963_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9g_27963/12_2022/8e9g_27963_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9g_27963/12_2022/8e9g_27963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9g_27963/12_2022/8e9g_27963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9g_27963/12_2022/8e9g_27963_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9g_27963/12_2022/8e9g_27963_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.036 sd= 0.182 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 35941 Number of models: 1 Model: "" Number of chains: 22 Chain: "O" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 884 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 113} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1334 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 168} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 930 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 114} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 21, 'TRANS': 198} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3037 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 384} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'GLU:plan': 16, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1595 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 209} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 5423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 5423 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 720} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 25, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 36, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 298 Chain: "F" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3110 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 403} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 166 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 19, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 172 Chain: "I" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1175 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 150} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 83 Chain: "H" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2911 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 103 Chain: "J" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1607 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "K" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 742 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 3853 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 208} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 602} Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 944 Unresolved non-hydrogen dihedrals: 607 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 16, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 9, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 387 Chain: "N" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3666 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 492} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 11, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 100 Chain: "M" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3695 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 488} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 2, 66 Unusual residues: {'MQ9': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'FES': 1, 'GTP': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' ZN': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1, 58 Unusual residues: {'MQ9': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'XP2': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1146 SG CYS B 38 53.244 82.242 100.634 1.00 65.13 S ATOM 1140 SG CYS B 37 58.072 80.505 100.682 1.00 67.50 S ATOM 1852 SG CYS B 132 55.805 78.883 95.523 1.00 60.98 S ATOM 1642 SG CYS B 103 53.268 75.652 99.137 1.00 62.31 S ATOM 8555 SG CYS E 107 75.158 59.527 29.370 1.00 95.44 S ATOM 8591 SG CYS E 112 77.952 60.257 27.109 1.00 97.96 S ATOM 8833 SG CYS E 148 77.869 55.244 31.583 1.00 97.12 S ATOM 8857 SG CYS E 152 80.517 55.956 29.576 1.00103.60 S ATOM 9701 SG CYS G 48 68.246 48.185 60.651 1.00 60.45 S ATOM 9776 SG CYS G 59 69.631 51.655 61.631 1.00 62.12 S ATOM 9802 SG CYS G 62 73.321 47.356 63.815 1.00 63.66 S ATOM 9893 SG CYS G 76 70.815 45.222 62.172 1.00 62.68 S ATOM 10167 SG CYS G 114 62.198 66.835 67.688 1.00 57.34 S ATOM 10224 SG CYS G 123 61.514 60.138 67.739 1.00 56.32 S ATOM 10188 SG CYS G 117 56.832 63.094 66.091 1.00 56.88 S ATOM 10909 SG CYS G 213 57.725 55.326 62.473 1.00 56.55 S ATOM 10561 SG CYS G 166 62.181 51.879 60.896 1.00 58.98 S ATOM 10540 SG CYS G 163 60.191 56.297 56.540 1.00 59.76 S ATOM 10583 SG CYS G 169 56.804 51.010 57.531 1.00 57.81 S ATOM 11103 SG CYS G 239 41.701 43.166 73.379 1.00 63.70 S ATOM 11149 SG CYS G 246 46.668 39.932 72.205 1.00 61.89 S ATOM 11363 SG CYS G 274 42.646 42.624 67.320 1.00 62.98 S ATOM 11128 SG CYS G 242 40.199 38.935 69.556 1.00 69.74 S ATOM 17240 SG CYS F 334 85.639 72.648 38.648 1.00 91.04 S ATOM 17906 SG CYS F 426 83.753 75.440 37.276 1.00 88.01 S ATOM 17403 SG CYS F 354 73.155 52.348 52.792 1.00 66.18 S ATOM 17719 SG CYS F 397 75.366 49.007 47.563 1.00 74.15 S ATOM 17423 SG CYS F 357 73.795 55.314 48.503 1.00 68.65 S ATOM 17384 SG CYS F 351 69.205 50.427 48.079 1.00 72.78 S ATOM 18679 SG CYS I 99 52.622 80.076 87.945 1.00 55.94 S ATOM 18697 SG CYS I 102 58.541 77.020 87.396 1.00 58.06 S ATOM 18715 SG CYS I 105 55.900 79.018 82.409 1.00 55.62 S ATOM 18411 SG CYS I 64 53.938 74.044 86.146 1.00 55.41 S ATOM 18358 SG CYS I 57 55.471 72.915 72.785 1.00 54.71 S ATOM 18739 SG CYS I 109 56.174 78.101 75.726 1.00 58.29 S ATOM 18381 SG CYS I 60 52.985 75.021 77.995 1.00 53.34 S ATOM 18340 SG CYS I 54 50.079 76.894 72.761 1.00 56.45 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 AMQ9 B 202 " occ=0.50 ... (56 atoms not shown) pdb=" O4 AMQ9 B 202 " occ=0.50 residue: pdb=" C1 BMQ9 H 501 " occ=0.50 ... (56 atoms not shown) pdb=" O4 BMQ9 H 501 " occ=0.50 Time building chain proxies: 20.02, per 1000 atoms: 0.56 Number of scatterers: 35941 At special positions: 0 Unit cell: (112.12, 147.526, 279.709, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 32 26.01 S 213 16.00 P 5 15.00 O 6167 8.00 N 6184 7.00 C 23339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.92 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1000 " pdb=" FE2 FES E1000 " - pdb=" SG CYS E 152 " pdb=" FE1 FES E1000 " - pdb=" SG CYS E 107 " pdb=" FE1 FES E1000 " - pdb=" SG CYS E 112 " pdb=" FE2 FES E1000 " - pdb=" SG CYS E 148 " pdb=" FES G 801 " pdb=" FE1 FES G 801 " - pdb=" SG CYS G 48 " pdb=" FE1 FES G 801 " - pdb=" SG CYS G 59 " pdb=" FE2 FES G 801 " - pdb=" SG CYS G 62 " pdb=" FE2 FES G 801 " - pdb=" SG CYS G 76 " pdb=" SF4 B 201 " pdb=" FE2 SF4 B 201 " - pdb=" SG CYS B 37 " pdb=" FE3 SF4 B 201 " - pdb=" SG CYS B 132 " pdb=" FE4 SF4 B 201 " - pdb=" SG CYS B 103 " pdb=" FE1 SF4 B 201 " - pdb=" SG CYS B 38 " pdb=" SF4 F 502 " pdb=" FE4 SF4 F 502 " - pdb=" SG CYS F 351 " pdb=" FE2 SF4 F 502 " - pdb=" SG CYS F 397 " pdb=" FE1 SF4 F 502 " - pdb=" SG CYS F 354 " pdb=" FE3 SF4 F 502 " - pdb=" SG CYS F 357 " pdb=" SF4 G 803 " pdb=" FE3 SF4 G 803 " - pdb=" NE2 HIS G 110 " pdb=" FE2 SF4 G 803 " - pdb=" SG CYS G 123 " pdb=" FE1 SF4 G 803 " - pdb=" SG CYS G 114 " pdb=" FE4 SF4 G 803 " - pdb=" SG CYS G 117 " pdb=" SF4 G 804 " pdb=" FE3 SF4 G 804 " - pdb=" SG CYS G 163 " pdb=" FE2 SF4 G 804 " - pdb=" SG CYS G 166 " pdb=" FE4 SF4 G 804 " - pdb=" SG CYS G 169 " pdb=" FE1 SF4 G 804 " - pdb=" SG CYS G 213 " pdb=" SF4 G 805 " pdb=" FE2 SF4 G 805 " - pdb=" SG CYS G 246 " pdb=" FE1 SF4 G 805 " - pdb=" SG CYS G 239 " pdb=" FE3 SF4 G 805 " - pdb=" SG CYS G 274 " pdb=" FE4 SF4 G 805 " - pdb=" SG CYS G 242 " pdb=" SF4 I 201 " pdb=" FE3 SF4 I 201 " - pdb=" NE2 HIS I 42 " pdb=" FE1 SF4 I 201 " - pdb=" SG CYS I 99 " pdb=" FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb=" FE2 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" FE4 SF4 I 201 " - pdb=" SG CYS I 64 " pdb=" SF4 I 202 " pdb=" FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb=" FE1 SF4 I 202 " - pdb=" SG CYS I 57 " pdb=" FE2 SF4 I 202 " - pdb=" SG CYS I 109 " pdb=" FE4 SF4 I 202 " - pdb=" SG CYS I 54 " Number of angles added : 93 Zn2+ tetrahedral coordination pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 426 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 421 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 334 " 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 219 helices and 26 sheets defined 55.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'O' and resid 16 through 25 Processing helix chain 'O' and resid 45 through 54 Processing helix chain 'O' and resid 71 through 81 Processing helix chain 'O' and resid 95 through 103 removed outlier: 3.792A pdb=" N TRP O 99 " --> pdb=" O ASP O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 127 Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 11 through 25 Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 52 through 55 Processing helix chain 'B' and resid 78 through 90 Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 136 through 151 Processing helix chain 'B' and resid 156 through 172 removed outlier: 3.893A pdb=" N ALA B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'A' and resid 5 through 27 Processing helix chain 'A' and resid 35 through 38 No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 65 through 86 removed outlier: 3.596A pdb=" N VAL A 73 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 88 through 91 No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 93 through 115 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 62 through 74 removed outlier: 3.786A pdb=" N ASP C 65 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'D' and resid 81 through 87 removed outlier: 4.041A pdb=" N GLU D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 99 removed outlier: 4.277A pdb=" N ARG D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 Proline residue: D 105 - end of helix Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 128 through 156 Processing helix chain 'D' and resid 160 through 181 removed outlier: 3.808A pdb=" N PHE D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 225 Proline residue: D 215 - end of helix removed outlier: 3.636A pdb=" N ASP D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 235 Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 254 through 259 removed outlier: 3.932A pdb=" N THR D 259 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 289 through 313 removed outlier: 3.592A pdb=" N HIS D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 354 through 365 Processing helix chain 'D' and resid 406 through 418 removed outlier: 4.039A pdb=" N GLN D 412 " --> pdb=" O PHE D 408 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA D 413 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA D 416 " --> pdb=" O GLN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 433 Processing helix chain 'D' and resid 437 through 441 Processing helix chain 'E' and resid 27 through 43 removed outlier: 3.761A pdb=" N GLN E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG E 43 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 61 removed outlier: 4.481A pdb=" N LEU E 52 " --> pdb=" O SER E 49 " (cutoff:3.500A) Proline residue: E 53 - end of helix removed outlier: 3.773A pdb=" N VAL E 58 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 77 Processing helix chain 'E' and resid 84 through 90 removed outlier: 3.546A pdb=" N PHE E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 114 Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 152 through 154 No H-bonds generated for 'chain 'E' and resid 152 through 154' Processing helix chain 'E' and resid 170 through 182 Processing helix chain 'E' and resid 196 through 203 Processing helix chain 'E' and resid 217 through 229 removed outlier: 4.586A pdb=" N GLY E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU E 224 " --> pdb=" O THR E 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 40 Processing helix chain 'G' and resid 93 through 108 Processing helix chain 'G' and resid 124 through 132 Processing helix chain 'G' and resid 168 through 174 Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 206 through 212 removed outlier: 3.630A pdb=" N VAL G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'G' and resid 275 through 279 Processing helix chain 'G' and resid 282 through 285 Processing helix chain 'G' and resid 306 through 319 Processing helix chain 'G' and resid 334 through 346 Processing helix chain 'G' and resid 362 through 371 Processing helix chain 'G' and resid 381 through 384 No H-bonds generated for 'chain 'G' and resid 381 through 384' Processing helix chain 'G' and resid 402 through 414 Processing helix chain 'G' and resid 428 through 432 Processing helix chain 'G' and resid 445 through 452 Processing helix chain 'G' and resid 456 through 459 No H-bonds generated for 'chain 'G' and resid 456 through 459' Processing helix chain 'G' and resid 469 through 473 Processing helix chain 'G' and resid 477 through 488 Processing helix chain 'G' and resid 499 through 506 removed outlier: 4.422A pdb=" N GLY G 503 " --> pdb=" O ALA G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 533 Processing helix chain 'G' and resid 546 through 554 Processing helix chain 'G' and resid 568 through 570 No H-bonds generated for 'chain 'G' and resid 568 through 570' Processing helix chain 'G' and resid 574 through 583 Processing helix chain 'G' and resid 596 through 600 Processing helix chain 'G' and resid 610 through 612 No H-bonds generated for 'chain 'G' and resid 610 through 612' Processing helix chain 'G' and resid 638 through 649 Processing helix chain 'G' and resid 658 through 668 Processing helix chain 'G' and resid 707 through 709 No H-bonds generated for 'chain 'G' and resid 707 through 709' Processing helix chain 'G' and resid 713 through 717 Processing helix chain 'G' and resid 728 through 733 Processing helix chain 'G' and resid 776 through 780 Processing helix chain 'F' and resid 8 through 11 removed outlier: 4.205A pdb=" N PHE F 11 " --> pdb=" O LEU F 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 8 through 11' Processing helix chain 'F' and resid 20 through 26 removed outlier: 3.547A pdb=" N HIS F 26 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 37 Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 62 through 67 Processing helix chain 'F' and resid 101 through 108 removed outlier: 3.508A pdb=" N LEU F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 124 Processing helix chain 'F' and resid 135 through 153 removed outlier: 3.835A pdb=" N LEU F 138 " --> pdb=" O GLY F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 205 through 208 No H-bonds generated for 'chain 'F' and resid 205 through 208' Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 220 through 230 Proline residue: F 227 - end of helix Processing helix chain 'F' and resid 233 through 238 removed outlier: 3.953A pdb=" N PHE F 237 " --> pdb=" O GLY F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 311 through 317 Processing helix chain 'F' and resid 335 through 349 Processing helix chain 'F' and resid 355 through 372 removed outlier: 3.654A pdb=" N TYR F 362 " --> pdb=" O ARG F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 391 removed outlier: 4.090A pdb=" N ASP F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 423 Proline residue: F 406 - end of helix removed outlier: 6.894A pdb=" N ASP F 416 " --> pdb=" O LYS F 412 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU F 417 " --> pdb=" O HIS F 413 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 422 " --> pdb=" O TYR F 418 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP F 423 " --> pdb=" O VAL F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 433 Processing helix chain 'I' and resid 5 through 19 removed outlier: 4.712A pdb=" N GLY I 10 " --> pdb=" O ALA I 7 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU I 15 " --> pdb=" O ALA I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 63 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 128 through 130 No H-bonds generated for 'chain 'I' and resid 128 through 130' Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'I' and resid 158 through 163 Processing helix chain 'H' and resid 14 through 47 Processing helix chain 'H' and resid 57 through 59 No H-bonds generated for 'chain 'H' and resid 57 through 59' Processing helix chain 'H' and resid 62 through 71 Processing helix chain 'H' and resid 83 through 103 Proline residue: H 90 - end of helix Proline residue: H 96 - end of helix removed outlier: 3.950A pdb=" N PHE H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER H 102 " --> pdb=" O PHE H 98 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL H 103 " --> pdb=" O VAL H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 148 removed outlier: 3.975A pdb=" N TYR H 140 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY H 141 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE H 142 " --> pdb=" O GLY H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 183 removed outlier: 4.933A pdb=" N ILE H 170 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA H 171 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE H 176 " --> pdb=" O MET H 172 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL H 177 " --> pdb=" O GLY H 173 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA H 178 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL H 179 " --> pdb=" O SER H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 195 Processing helix chain 'H' and resid 200 through 203 No H-bonds generated for 'chain 'H' and resid 200 through 203' Processing helix chain 'H' and resid 205 through 218 Processing helix chain 'H' and resid 230 through 233 No H-bonds generated for 'chain 'H' and resid 230 through 233' Processing helix chain 'H' and resid 236 through 238 No H-bonds generated for 'chain 'H' and resid 236 through 238' Processing helix chain 'H' and resid 243 through 268 Processing helix chain 'H' and resid 276 through 279 No H-bonds generated for 'chain 'H' and resid 276 through 279' Processing helix chain 'H' and resid 289 through 311 Processing helix chain 'H' and resid 317 through 326 Processing helix chain 'H' and resid 328 through 348 Processing helix chain 'H' and resid 351 through 374 removed outlier: 4.408A pdb=" N LEU H 358 " --> pdb=" O ALA H 355 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL H 366 " --> pdb=" O VAL H 363 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE H 369 " --> pdb=" O VAL H 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 39 Processing helix chain 'J' and resid 43 through 63 Processing helix chain 'J' and resid 67 through 91 Processing helix chain 'J' and resid 107 through 126 Processing helix chain 'J' and resid 130 through 132 No H-bonds generated for 'chain 'J' and resid 130 through 132' Processing helix chain 'J' and resid 137 through 141 removed outlier: 3.651A pdb=" N ASN J 141 " --> pdb=" O ALA J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 155 Processing helix chain 'J' and resid 158 through 178 removed outlier: 3.791A pdb=" N SER J 165 " --> pdb=" O PHE J 161 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 185 No H-bonds generated for 'chain 'J' and resid 183 through 185' Processing helix chain 'J' and resid 190 through 194 Processing helix chain 'J' and resid 199 through 202 No H-bonds generated for 'chain 'J' and resid 199 through 202' Processing helix chain 'J' and resid 232 through 234 No H-bonds generated for 'chain 'J' and resid 232 through 234' Processing helix chain 'K' and resid 3 through 23 removed outlier: 3.837A pdb=" N PHE K 14 " --> pdb=" O ALA K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 52 Processing helix chain 'K' and resid 56 through 86 removed outlier: 3.708A pdb=" N THR K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 24 removed outlier: 4.196A pdb=" N LEU L 14 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Proline residue: L 15 - end of helix Processing helix chain 'L' and resid 26 through 29 Processing helix chain 'L' and resid 33 through 56 Processing helix chain 'L' and resid 60 through 63 Processing helix chain 'L' and resid 88 through 111 removed outlier: 3.666A pdb=" N CYS L 92 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE L 93 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 137 Processing helix chain 'L' and resid 141 through 159 Processing helix chain 'L' and resid 166 through 197 Processing helix chain 'L' and resid 202 through 209 Processing helix chain 'L' and resid 214 through 232 Processing helix chain 'L' and resid 240 through 246 removed outlier: 3.750A pdb=" N MET L 245 " --> pdb=" O LEU L 241 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU L 246 " --> pdb=" O GLY L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 257 Processing helix chain 'L' and resid 261 through 270 removed outlier: 3.713A pdb=" N ARG L 270 " --> pdb=" O LEU L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 276 Processing helix chain 'L' and resid 279 through 302 removed outlier: 3.882A pdb=" N ALA L 302 " --> pdb=" O ILE L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 326 Processing helix chain 'L' and resid 328 through 359 removed outlier: 5.415A pdb=" N ALA L 333 " --> pdb=" O ALA L 330 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS L 346 " --> pdb=" O GLY L 343 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 375 No H-bonds generated for 'chain 'L' and resid 372 through 375' Processing helix chain 'L' and resid 377 through 391 Processing helix chain 'L' and resid 397 through 412 removed outlier: 3.717A pdb=" N SER L 401 " --> pdb=" O ALA L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 443 Processing helix chain 'L' and resid 460 through 491 Proline residue: L 465 - end of helix removed outlier: 5.382A pdb=" N GLY L 477 " --> pdb=" O SER L 473 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY L 478 " --> pdb=" O VAL L 474 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY L 483 " --> pdb=" O ALA L 479 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY L 484 " --> pdb=" O LEU L 480 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR L 485 " --> pdb=" O ALA L 481 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU L 486 " --> pdb=" O ILE L 482 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER L 487 " --> pdb=" O GLY L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 505 through 527 Processing helix chain 'L' and resid 541 through 547 Processing helix chain 'L' and resid 549 through 577 removed outlier: 5.757A pdb=" N ASP L 553 " --> pdb=" O LEU L 550 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE L 555 " --> pdb=" O GLY L 552 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL L 559 " --> pdb=" O ASN L 556 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE L 560 " --> pdb=" O GLU L 557 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N MET L 561 " --> pdb=" O ALA L 558 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG L 562 " --> pdb=" O VAL L 559 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY L 563 " --> pdb=" O PHE L 560 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS L 577 " --> pdb=" O VAL L 574 " (cutoff:3.500A) Processing helix chain 'L' and resid 579 through 600 removed outlier: 3.865A pdb=" N ALA L 583 " --> pdb=" O VAL L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 605 through 627 removed outlier: 3.942A pdb=" N GLY L 615 " --> pdb=" O SER L 611 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER L 616 " --> pdb=" O MET L 612 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA L 617 " --> pdb=" O LEU L 613 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU L 618 " --> pdb=" O GLY L 614 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL L 626 " --> pdb=" O ALA L 622 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN L 627 " --> pdb=" O ILE L 623 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 30 Proline residue: N 13 - end of helix removed outlier: 6.309A pdb=" N VAL N 17 " --> pdb=" O PRO N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 63 removed outlier: 5.196A pdb=" N TYR N 37 " --> pdb=" O GLN N 34 " (cutoff:3.500A) Proline residue: N 38 - end of helix removed outlier: 3.873A pdb=" N VAL N 41 " --> pdb=" O PRO N 38 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA N 44 " --> pdb=" O VAL N 41 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU N 45 " --> pdb=" O THR N 42 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY N 46 " --> pdb=" O LEU N 43 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA N 50 " --> pdb=" O GLY N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 99 Processing helix chain 'N' and resid 129 through 137 Processing helix chain 'N' and resid 142 through 160 Proline residue: N 146 - end of helix Proline residue: N 159 - end of helix Processing helix chain 'N' and resid 164 through 183 Proline residue: N 177 - end of helix removed outlier: 3.987A pdb=" N GLY N 183 " --> pdb=" O TYR N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 189 through 221 Processing helix chain 'N' and resid 226 through 235 Processing helix chain 'N' and resid 242 through 258 Processing helix chain 'N' and resid 261 through 263 No H-bonds generated for 'chain 'N' and resid 261 through 263' Processing helix chain 'N' and resid 265 through 273 removed outlier: 4.168A pdb=" N ASP N 269 " --> pdb=" O SER N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 299 removed outlier: 3.633A pdb=" N ALA N 284 " --> pdb=" O ALA N 280 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 329 Proline residue: N 311 - end of helix removed outlier: 3.558A pdb=" N ALA N 315 " --> pdb=" O PRO N 311 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR N 325 " --> pdb=" O MET N 321 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA N 328 " --> pdb=" O GLY N 324 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 355 removed outlier: 3.512A pdb=" N ALA N 355 " --> pdb=" O THR N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 384 removed outlier: 3.568A pdb=" N LEU N 384 " --> pdb=" O ALA N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 399 Processing helix chain 'N' and resid 402 through 405 No H-bonds generated for 'chain 'N' and resid 402 through 405' Processing helix chain 'N' and resid 407 through 421 Processing helix chain 'N' and resid 427 through 441 Processing helix chain 'N' and resid 445 through 470 removed outlier: 3.932A pdb=" N TYR N 460 " --> pdb=" O ALA N 456 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE N 461 " --> pdb=" O VAL N 457 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL N 465 " --> pdb=" O PHE N 461 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE N 466 " --> pdb=" O TYR N 462 " (cutoff:3.500A) Processing helix chain 'N' and resid 486 through 504 Processing helix chain 'N' and resid 507 through 515 removed outlier: 6.315A pdb=" N LEU N 512 " --> pdb=" O PRO N 508 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 24 Proline residue: M 15 - end of helix Processing helix chain 'M' and resid 27 through 54 removed outlier: 3.605A pdb=" N GLN M 30 " --> pdb=" O ALA M 27 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL M 31 " --> pdb=" O ALA M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 74 No H-bonds generated for 'chain 'M' and resid 72 through 74' Processing helix chain 'M' and resid 84 through 103 Proline residue: M 98 - end of helix Processing helix chain 'M' and resid 114 through 116 No H-bonds generated for 'chain 'M' and resid 114 through 116' Processing helix chain 'M' and resid 118 through 138 Processing helix chain 'M' and resid 142 through 161 removed outlier: 4.329A pdb=" N LEU M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE M 154 " --> pdb=" O GLU M 150 " (cutoff:3.500A) Proline residue: M 155 - end of helix Processing helix chain 'M' and resid 166 through 198 removed outlier: 4.585A pdb=" N SER M 169 " --> pdb=" O GLU M 166 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN M 179 " --> pdb=" O LEU M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 219 Processing helix chain 'M' and resid 226 through 243 Processing helix chain 'M' and resid 249 through 259 removed outlier: 4.416A pdb=" N TRP M 252 " --> pdb=" O PHE M 249 " (cutoff:3.500A) Proline residue: M 254 - end of helix removed outlier: 3.547A pdb=" N GLU M 259 " --> pdb=" O ALA M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 270 Processing helix chain 'M' and resid 272 through 282 removed outlier: 3.769A pdb=" N PHE M 278 " --> pdb=" O VAL M 275 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG M 282 " --> pdb=" O GLY M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 287 No H-bonds generated for 'chain 'M' and resid 284 through 287' Processing helix chain 'M' and resid 289 through 316 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 320 through 340 Processing helix chain 'M' and resid 344 through 374 Processing helix chain 'M' and resid 380 through 382 No H-bonds generated for 'chain 'M' and resid 380 through 382' Processing helix chain 'M' and resid 386 through 389 No H-bonds generated for 'chain 'M' and resid 386 through 389' Processing helix chain 'M' and resid 391 through 404 Processing helix chain 'M' and resid 411 through 426 removed outlier: 3.615A pdb=" N SER M 415 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG M 426 " --> pdb=" O GLY M 422 " (cutoff:3.500A) Processing helix chain 'M' and resid 428 through 453 removed outlier: 4.103A pdb=" N ALA M 437 " --> pdb=" O PHE M 433 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU M 438 " --> pdb=" O ALA M 434 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL M 439 " --> pdb=" O ALA M 435 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR M 448 " --> pdb=" O TYR M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 473 through 491 Proline residue: M 481 - end of helix Processing helix chain 'M' and resid 493 through 511 removed outlier: 3.768A pdb=" N ASP M 498 " --> pdb=" O PRO M 495 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN M 501 " --> pdb=" O ASP M 498 " (cutoff:3.500A) Proline residue: M 502 - end of helix removed outlier: 3.560A pdb=" N THR M 509 " --> pdb=" O HIS M 506 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'O' and resid 37 through 42 removed outlier: 6.200A pdb=" N LEU O 7 " --> pdb=" O GLU O 38 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL O 40 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE O 9 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL O 42 " --> pdb=" O ILE O 9 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL O 11 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU O 59 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N TYR O 12 " --> pdb=" O LEU O 59 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE O 61 " --> pdb=" O TYR O 12 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU O 62 " --> pdb=" O PRO O 87 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU O 89 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA O 108 " --> pdb=" O VAL O 90 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR O 92 " --> pdb=" O ALA O 108 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL O 110 " --> pdb=" O THR O 92 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.870A pdb=" N TRP B 96 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 127 " --> pdb=" O ALA B 99 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 125 through 128 removed outlier: 5.231A pdb=" N LEU C 94 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA C 157 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 221 through 223 Processing sheet with id= E, first strand: chain 'C' and resid 23 through 29 removed outlier: 4.135A pdb=" N GLU C 23 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 50 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL C 27 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG C 48 " --> pdb=" O VAL C 27 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 41 through 44 removed outlier: 3.524A pdb=" N GLU D 69 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU D 63 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 332 through 335 Processing sheet with id= H, first strand: chain 'D' and resid 373 through 381 Processing sheet with id= I, first strand: chain 'E' and resid 141 through 146 removed outlier: 6.812A pdb=" N TYR E 102 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU E 144 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL E 104 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL E 146 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL E 106 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 15 through 20 Processing sheet with id= K, first strand: chain 'G' and resid 156 through 158 Processing sheet with id= L, first strand: chain 'G' and resid 183 through 185 Processing sheet with id= M, first strand: chain 'G' and resid 233 through 238 removed outlier: 6.291A pdb=" N ARG G 253 " --> pdb=" O VAL G 257 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL G 257 " --> pdb=" O ARG G 253 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 294 through 297 Processing sheet with id= O, first strand: chain 'G' and resid 324 through 327 removed outlier: 6.686A pdb=" N ALA G 560 " --> pdb=" O GLY G 325 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU G 327 " --> pdb=" O ALA G 560 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU G 562 " --> pdb=" O LEU G 327 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE G 586 " --> pdb=" O LEU G 561 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL G 563 " --> pdb=" O PHE G 586 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL G 588 " --> pdb=" O VAL G 563 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL G 603 " --> pdb=" O SER G 589 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU G 591 " --> pdb=" O VAL G 603 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE G 605 " --> pdb=" O GLU G 591 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 418 through 422 removed outlier: 6.829A pdb=" N VAL G 464 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA G 393 " --> pdb=" O VAL G 464 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU G 466 " --> pdb=" O ALA G 393 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG G 491 " --> pdb=" O ILE G 465 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL G 467 " --> pdb=" O ARG G 491 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA G 493 " --> pdb=" O VAL G 467 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 615 through 618 Processing sheet with id= R, first strand: chain 'G' and resid 764 through 768 removed outlier: 7.360A pdb=" N VAL G 765 " --> pdb=" O GLN G 693 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL G 695 " --> pdb=" O VAL G 765 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU G 767 " --> pdb=" O VAL G 695 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA G 697 " --> pdb=" O LEU G 767 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 215 through 219 removed outlier: 6.778A pdb=" N TYR F 87 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ASN F 218 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL F 89 " --> pdb=" O ASN F 218 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG F 127 " --> pdb=" O HIS F 86 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU F 88 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA F 129 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE F 90 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE F 131 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA F 92 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL F 133 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASP F 169 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE F 131 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE F 171 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL F 133 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS F 173 " --> pdb=" O VAL F 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 248 through 253 Processing sheet with id= U, first strand: chain 'F' and resid 299 through 301 removed outlier: 7.008A pdb=" N PHE F 329 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP F 290 " --> pdb=" O GLN F 327 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLN F 327 " --> pdb=" O TRP F 290 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 42 through 44 Processing sheet with id= W, first strand: chain 'I' and resid 69 through 75 removed outlier: 6.613A pdb=" N ALA I 74 " --> pdb=" O GLY I 89 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLY I 89 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 109 through 112 Processing sheet with id= Y, first strand: chain 'L' and resid 65 through 71 removed outlier: 7.020A pdb=" N PHE L 82 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 66 through 71 removed outlier: 4.017A pdb=" N TRP M 70 " --> pdb=" O THR M 76 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR M 76 " --> pdb=" O TRP M 70 " (cutoff:3.500A) 1907 hydrogen bonds defined for protein. 4869 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: 13.69 Time building geometry restraints manager: 17.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 14476 1.39 - 1.62: 21958 1.62 - 1.84: 304 1.84 - 2.06: 0 2.06 - 2.29: 92 Bond restraints: 36830 Sorted by residual: bond pdb=" C4A FMN F 503 " pdb=" N5 FMN F 503 " ideal model delta sigma weight residual 1.380 1.304 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C07 XP2 L 701 " pdb=" O08 XP2 L 701 " ideal model delta sigma weight residual 1.395 1.465 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C10 FMN F 503 " pdb=" N1 FMN F 503 " ideal model delta sigma weight residual 1.380 1.311 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C58 XP2 L 701 " pdb=" C59 XP2 L 701 " ideal model delta sigma weight residual 1.537 1.603 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C42 XP2 L 701 " pdb=" C43 XP2 L 701 " ideal model delta sigma weight residual 1.528 1.591 -0.063 2.00e-02 2.50e+03 9.92e+00 ... (remaining 36825 not shown) Histogram of bond angle deviations from ideal: 73.50 - 85.61: 88 85.61 - 97.73: 1 97.73 - 109.84: 5017 109.84 - 121.96: 38861 121.96 - 134.07: 6592 Bond angle restraints: 50559 Sorted by residual: angle pdb=" N PRO E 235 " pdb=" CA PRO E 235 " pdb=" CB PRO E 235 " ideal model delta sigma weight residual 103.25 94.97 8.28 1.05e+00 9.07e-01 6.21e+01 angle pdb=" C PRO E 235 " pdb=" CA PRO E 235 " pdb=" CB PRO E 235 " ideal model delta sigma weight residual 111.56 103.03 8.53 1.65e+00 3.67e-01 2.67e+01 angle pdb=" N ILE B 52 " pdb=" CA ILE B 52 " pdb=" C ILE B 52 " ideal model delta sigma weight residual 111.05 106.88 4.17 1.25e+00 6.40e-01 1.11e+01 angle pdb=" N ILE C 199 " pdb=" CA ILE C 199 " pdb=" C ILE C 199 " ideal model delta sigma weight residual 111.90 109.32 2.58 8.10e-01 1.52e+00 1.01e+01 angle pdb=" N MET M 354 " pdb=" CA MET M 354 " pdb=" C MET M 354 " ideal model delta sigma weight residual 111.11 107.30 3.81 1.20e+00 6.94e-01 1.01e+01 ... (remaining 50554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 21109 34.38 - 68.76: 196 68.76 - 103.14: 18 103.14 - 137.53: 1 137.53 - 171.91: 2 Dihedral angle restraints: 21326 sinusoidal: 7005 harmonic: 14321 Sorted by residual: dihedral pdb=" C10 FMN F 503 " pdb=" C1' FMN F 503 " pdb=" N10 FMN F 503 " pdb=" C2' FMN F 503 " ideal model delta sinusoidal sigma weight residual 257.59 85.68 171.91 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP G 802 " pdb=" C1' GTP G 802 " pdb=" N9 GTP G 802 " pdb=" O4' GTP G 802 " ideal model delta sinusoidal sigma weight residual 104.59 -97.31 -158.10 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' FMN F 503 " pdb=" O5' FMN F 503 " pdb=" P FMN F 503 " pdb=" O1P FMN F 503 " ideal model delta sinusoidal sigma weight residual 75.26 -172.30 -112.44 1 2.00e+01 2.50e-03 3.32e+01 ... (remaining 21323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.023: 6093 1.023 - 2.045: 0 2.045 - 3.068: 0 3.068 - 4.090: 0 4.090 - 5.113: 2 Chirality restraints: 6095 Sorted by residual: chirality pdb=" C32 XP2 L 701 " pdb=" C07 XP2 L 701 " pdb=" C64 XP2 L 701 " pdb=" O33 XP2 L 701 " both_signs ideal model delta sigma weight residual False -2.54 2.57 -5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" C03 XP2 L 701 " pdb=" C02 XP2 L 701 " pdb=" C05 XP2 L 701 " pdb=" O04 XP2 L 701 " both_signs ideal model delta sigma weight residual False -2.51 2.53 -5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" CA PRO E 235 " pdb=" N PRO E 235 " pdb=" C PRO E 235 " pdb=" CB PRO E 235 " both_signs ideal model delta sigma weight residual False 2.72 2.91 -0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 6092 not shown) Planarity restraints: 6394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 AMQ9 B 202 " -0.078 2.00e-02 2.50e+03 1.99e-01 1.39e+03 pdb=" C2 AMQ9 B 202 " -0.037 2.00e-02 2.50e+03 pdb=" C3 AMQ9 B 202 " 0.032 2.00e-02 2.50e+03 pdb=" C3AAMQ9 B 202 " 0.077 2.00e-02 2.50e+03 pdb=" C3BAMQ9 B 202 " 0.051 2.00e-02 2.50e+03 pdb=" C3CAMQ9 B 202 " -0.015 2.00e-02 2.50e+03 pdb=" C3DAMQ9 B 202 " -0.055 2.00e-02 2.50e+03 pdb=" C4 AMQ9 B 202 " 0.047 2.00e-02 2.50e+03 pdb=" C5 AMQ9 B 202 " -0.082 2.00e-02 2.50e+03 pdb=" C5MAMQ9 B 202 " -0.436 2.00e-02 2.50e+03 pdb=" C6 AMQ9 B 202 " 0.105 2.00e-02 2.50e+03 pdb=" C7 AMQ9 B 202 " 0.495 2.00e-02 2.50e+03 pdb=" O1 AMQ9 B 202 " -0.244 2.00e-02 2.50e+03 pdb=" O4 AMQ9 B 202 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BMQ9 H 501 " -0.034 2.00e-02 2.50e+03 1.91e-01 1.28e+03 pdb=" C2 BMQ9 H 501 " 0.004 2.00e-02 2.50e+03 pdb=" C3 BMQ9 H 501 " -0.049 2.00e-02 2.50e+03 pdb=" C3ABMQ9 H 501 " -0.012 2.00e-02 2.50e+03 pdb=" C3BBMQ9 H 501 " 0.072 2.00e-02 2.50e+03 pdb=" C3CBMQ9 H 501 " 0.120 2.00e-02 2.50e+03 pdb=" C3DBMQ9 H 501 " 0.086 2.00e-02 2.50e+03 pdb=" C4 BMQ9 H 501 " -0.133 2.00e-02 2.50e+03 pdb=" C5 BMQ9 H 501 " 0.104 2.00e-02 2.50e+03 pdb=" C5MBMQ9 H 501 " 0.518 2.00e-02 2.50e+03 pdb=" C6 BMQ9 H 501 " -0.041 2.00e-02 2.50e+03 pdb=" C7 BMQ9 H 501 " -0.198 2.00e-02 2.50e+03 pdb=" O1 BMQ9 H 501 " -0.063 2.00e-02 2.50e+03 pdb=" O4 BMQ9 H 501 " -0.374 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C42AMQ9 B 202 " 0.264 2.00e-02 2.50e+03 2.22e-01 6.18e+02 pdb=" C43AMQ9 B 202 " -0.374 2.00e-02 2.50e+03 pdb=" C44AMQ9 B 202 " -0.077 2.00e-02 2.50e+03 pdb=" C45AMQ9 B 202 " 0.177 2.00e-02 2.50e+03 pdb=" C46AMQ9 B 202 " 0.010 2.00e-02 2.50e+03 ... (remaining 6391 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 156 2.47 - 3.08: 28568 3.08 - 3.68: 59958 3.68 - 4.29: 90163 4.29 - 4.90: 147300 Nonbonded interactions: 326145 Sorted by model distance: nonbonded pdb=" OE2 GLU F 372 " pdb="ZN ZN F 501 " model vdw 1.861 2.230 nonbonded pdb=" OG1 THR F 270 " pdb=" OE1 GLU F 273 " model vdw 1.934 2.440 nonbonded pdb=" OG SER N 341 " pdb=" OH TYR N 462 " model vdw 1.981 2.440 nonbonded pdb=" OD2 ASP H 123 " pdb=" OG SER H 187 " model vdw 2.046 2.440 nonbonded pdb=" O TRP D 90 " pdb=" OG1 THR D 91 " model vdw 2.048 2.440 ... (remaining 326140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 32 7.16 5 Zn 1 6.06 5 P 5 5.49 5 S 213 5.16 5 C 23339 2.51 5 N 6184 2.21 5 O 6167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 14.890 Check model and map are aligned: 0.520 Convert atoms to be neutral: 0.290 Process input model: 108.970 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 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 0.076 36830 Z= 0.289 Angle : 0.615 8.533 50559 Z= 0.348 Chirality : 0.100 5.113 6095 Planarity : 0.008 0.222 6394 Dihedral : 11.510 171.908 12186 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.78 % Favored : 96.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.15 % 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: 1.13 (0.12), residues: 5021 helix: 1.37 (0.10), residues: 2833 sheet: 0.03 (0.32), residues: 270 loop : 0.05 (0.15), residues: 1918 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 4.027 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 1.5346 time to fit residues: 288.2762 Evaluate side-chains 151 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 4.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 0.8980 chunk 377 optimal weight: 20.0000 chunk 209 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 254 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 390 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 290 optimal weight: 3.9990 chunk 452 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 36830 Z= 0.262 Angle : 0.587 11.301 50559 Z= 0.295 Chirality : 0.042 0.396 6095 Planarity : 0.005 0.127 6394 Dihedral : 7.010 171.598 5517 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.15 % Favored : 96.73 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: 1.14 (0.12), residues: 5021 helix: 1.26 (0.10), residues: 2851 sheet: 0.20 (0.33), residues: 258 loop : 0.22 (0.16), residues: 1912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 4.041 Fit side-chains outliers start: 12 outliers final: 1 residues processed: 152 average time/residue: 1.5071 time to fit residues: 282.9971 Evaluate side-chains 152 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 3.744 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.3255 time to fit residues: 6.4416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 0.0370 chunk 140 optimal weight: 2.9990 chunk 376 optimal weight: 20.0000 chunk 307 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 453 optimal weight: 0.0040 chunk 489 optimal weight: 6.9990 chunk 403 optimal weight: 2.9990 chunk 449 optimal weight: 3.9990 chunk 154 optimal weight: 0.3980 chunk 363 optimal weight: 30.0000 overall best weight: 0.8072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 36830 Z= 0.178 Angle : 0.524 9.386 50559 Z= 0.264 Chirality : 0.040 0.428 6095 Planarity : 0.005 0.126 6394 Dihedral : 6.759 167.257 5517 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.97 % Favored : 96.91 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: 1.20 (0.12), residues: 5021 helix: 1.30 (0.10), residues: 2848 sheet: 0.35 (0.33), residues: 255 loop : 0.26 (0.16), residues: 1918 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 4.507 Fit side-chains outliers start: 22 outliers final: 0 residues processed: 165 average time/residue: 1.4018 time to fit residues: 288.2628 Evaluate side-chains 151 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 4.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 0.9980 chunk 340 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 304 optimal weight: 8.9990 chunk 454 optimal weight: 9.9990 chunk 481 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 430 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN ** G 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 36830 Z= 0.217 Angle : 0.527 9.701 50559 Z= 0.264 Chirality : 0.040 0.436 6095 Planarity : 0.005 0.123 6394 Dihedral : 6.619 166.846 5517 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.03 % Favored : 96.87 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: 1.22 (0.12), residues: 5021 helix: 1.31 (0.10), residues: 2850 sheet: 0.34 (0.33), residues: 256 loop : 0.27 (0.16), residues: 1915 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 4.491 Fit side-chains outliers start: 30 outliers final: 7 residues processed: 166 average time/residue: 1.4733 time to fit residues: 306.2367 Evaluate side-chains 158 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 4.061 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 1.4716 time to fit residues: 10.4204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 358 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 410 optimal weight: 0.8980 chunk 332 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 432 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 36830 Z= 0.205 Angle : 0.520 9.705 50559 Z= 0.259 Chirality : 0.040 0.437 6095 Planarity : 0.005 0.121 6394 Dihedral : 6.506 166.397 5517 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: 1.24 (0.12), residues: 5021 helix: 1.32 (0.10), residues: 2859 sheet: 0.48 (0.33), residues: 256 loop : 0.26 (0.16), residues: 1906 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 4.108 Fit side-chains outliers start: 29 outliers final: 5 residues processed: 171 average time/residue: 1.3670 time to fit residues: 292.2593 Evaluate side-chains 157 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 4.089 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 5.2673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 4.9990 chunk 433 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 282 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 481 optimal weight: 10.0000 chunk 399 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 59 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 36830 Z= 0.433 Angle : 0.614 10.148 50559 Z= 0.306 Chirality : 0.043 0.437 6095 Planarity : 0.005 0.122 6394 Dihedral : 6.652 166.653 5517 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: 1.20 (0.12), residues: 5021 helix: 1.28 (0.10), residues: 2844 sheet: 0.36 (0.32), residues: 269 loop : 0.28 (0.16), residues: 1908 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 4.408 Fit side-chains outliers start: 35 outliers final: 13 residues processed: 168 average time/residue: 1.4497 time to fit residues: 304.1974 Evaluate side-chains 164 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 4.119 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 1.5534 time to fit residues: 10.6591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 351 optimal weight: 0.9990 chunk 272 optimal weight: 0.6980 chunk 405 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 chunk 479 optimal weight: 0.9980 chunk 300 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 36830 Z= 0.181 Angle : 0.522 9.656 50559 Z= 0.261 Chirality : 0.040 0.432 6095 Planarity : 0.005 0.120 6394 Dihedral : 6.529 167.157 5517 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: 1.25 (0.12), residues: 5021 helix: 1.31 (0.10), residues: 2844 sheet: 0.41 (0.33), residues: 268 loop : 0.32 (0.16), residues: 1909 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 4.092 Fit side-chains outliers start: 28 outliers final: 11 residues processed: 171 average time/residue: 1.3880 time to fit residues: 298.8226 Evaluate side-chains 162 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 4.002 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 1.4034 time to fit residues: 6.7616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 305 optimal weight: 8.9990 chunk 327 optimal weight: 0.9990 chunk 237 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 377 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 36830 Z= 0.294 Angle : 0.552 9.661 50559 Z= 0.274 Chirality : 0.041 0.426 6095 Planarity : 0.005 0.119 6394 Dihedral : 6.498 167.280 5517 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: 1.26 (0.12), residues: 5021 helix: 1.32 (0.10), residues: 2837 sheet: 0.41 (0.33), residues: 268 loop : 0.32 (0.16), residues: 1916 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 4.143 Fit side-chains outliers start: 32 outliers final: 12 residues processed: 171 average time/residue: 1.4013 time to fit residues: 302.8915 Evaluate side-chains 163 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 4.077 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 1.7165 time to fit residues: 7.3488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 2.9990 chunk 459 optimal weight: 8.9990 chunk 419 optimal weight: 10.0000 chunk 447 optimal weight: 0.9990 chunk 269 optimal weight: 0.0980 chunk 194 optimal weight: 5.9990 chunk 351 optimal weight: 3.9990 chunk 137 optimal weight: 0.0370 chunk 404 optimal weight: 5.9990 chunk 423 optimal weight: 0.7980 chunk 445 optimal weight: 0.7980 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.079 36830 Z= 0.164 Angle : 0.516 9.430 50559 Z= 0.256 Chirality : 0.039 0.414 6095 Planarity : 0.005 0.118 6394 Dihedral : 6.378 167.573 5517 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.03 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: 1.31 (0.12), residues: 5021 helix: 1.37 (0.10), residues: 2830 sheet: 0.43 (0.32), residues: 288 loop : 0.35 (0.16), residues: 1903 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 4.062 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 169 average time/residue: 1.4593 time to fit residues: 307.2312 Evaluate side-chains 162 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 4.052 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 1.4437 time to fit residues: 7.0750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 0.9980 chunk 472 optimal weight: 0.8980 chunk 288 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 496 optimal weight: 4.9990 chunk 456 optimal weight: 0.8980 chunk 395 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 36830 Z= 0.270 Angle : 0.544 11.157 50559 Z= 0.270 Chirality : 0.041 0.408 6095 Planarity : 0.005 0.117 6394 Dihedral : 6.373 167.496 5517 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: 1.34 (0.12), residues: 5021 helix: 1.38 (0.10), residues: 2829 sheet: 0.45 (0.32), residues: 278 loop : 0.38 (0.16), residues: 1914 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10042 Ramachandran restraints generated. 5021 Oldfield, 0 Emsley, 5021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 4.292 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 162 average time/residue: 1.4454 time to fit residues: 293.4875 Evaluate side-chains 162 residues out of total 3933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 4.018 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 5.3031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 313 optimal weight: 9.9990 chunk 420 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 364 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 395 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 406 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.036857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.030867 restraints weight = 262396.566| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.34 r_work: 0.2929 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 36830 Z= 0.223 Angle : 0.529 9.998 50559 Z= 0.263 Chirality : 0.040 0.395 6095 Planarity : 0.004 0.116 6394 Dihedral : 6.357 167.494 5517 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.79 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: 1.33 (0.12), residues: 5021 helix: 1.37 (0.10), residues: 2830 sheet: 0.48 (0.32), residues: 278 loop : 0.37 (0.16), residues: 1913 =============================================================================== Job complete usr+sys time: 8259.86 seconds wall clock time: 149 minutes 35.26 seconds (8975.26 seconds total)