Starting phenix.real_space_refine on Mon Mar 25 17:56:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/03_2024/6gmh_0031_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/03_2024/6gmh_0031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/03_2024/6gmh_0031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/03_2024/6gmh_0031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/03_2024/6gmh_0031_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gmh_0031/03_2024/6gmh_0031_neut_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 108 5.49 5 Mg 1 5.21 5 S 235 5.16 5 C 30458 2.51 5 N 9346 2.21 5 O 10082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1149": "NH1" <-> "NH2" Residue "A ARG 1153": "NH1" <-> "NH2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A ARG 1213": "NH1" <-> "NH2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A PHE 1471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 763": "NH1" <-> "NH2" Residue "Q ARG 830": "NH1" <-> "NH2" Residue "W ARG 50": "NH1" <-> "NH2" Residue "W PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 147": "NH1" <-> "NH2" Residue "Z ARG 198": "NH1" <-> "NH2" Residue "Z ARG 555": "NH1" <-> "NH2" Residue "Z ARG 571": "NH1" <-> "NH2" Residue "Z ARG 577": "NH1" <-> "NH2" Residue "Z ARG 582": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50239 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1441, 11371 Classifications: {'peptide': 1441} Link IDs: {'PCIS': 1, 'PTRANS': 72, 'TRANS': 1367} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 9052 Classifications: {'peptide': 1132} Link IDs: {'PTRANS': 53, 'TRANS': 1078} Chain breaks: 4 Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2115 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 15, 'TRANS': 247} Chain breaks: 1 Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 4737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 4737 Classifications: {'peptide': 1002} Incomplete info: {'backbone_only': 780, 'n_c_alpha_c_only': 11, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 43, 'TRANS': 958} Chain breaks: 12 Unresolved chain link angles: 44 Unresolved non-hydrogen bonds: 3621 Unresolved non-hydrogen angles: 5183 Unresolved non-hydrogen dihedrals: 2341 Unresolved non-hydrogen chiralities: 1013 Planarities with less than four sites: {'GLN:plan1': 42, 'HIS:plan': 19, 'UNK:plan-1': 8, 'TYR:plan': 32, 'ASN:plan1': 30, 'TRP:plan': 8, 'ASP:plan': 52, 'PHE:plan': 35, 'GLU:plan': 82, 'ARG:plan': 58} Unresolved non-hydrogen planarities: 1817 Chain: "N" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 773 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Chain: "P" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 452 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 6, 'rna3p': 14} Chain: "Q" Number of atoms: 4116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 884, 4116 Classifications: {'peptide': 884} Incomplete info: {'backbone_only': 730} Link IDs: {'PTRANS': 11, 'TRANS': 872} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 2853 Unresolved non-hydrogen angles: 4312 Unresolved non-hydrogen dihedrals: 1601 Unresolved non-hydrogen chiralities: 830 Planarities with less than four sites: {'GLN:plan1': 33, 'ASN:plan1': 20, 'ASP:plan': 24, 'TYR:plan': 30, 'UNK:plan-1': 300, 'TRP:plan': 6, 'HIS:plan': 15, 'PHE:plan': 17, 'GLU:plan': 35, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 1367 Chain: "T" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 974 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "U" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 440 Classifications: {'peptide': 110} Incomplete info: {'backbone_only': 110} Link IDs: {'TRANS': 109} Chain breaks: 3 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 550 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'UNK:plan-1': 110} Unresolved non-hydrogen planarities: 110 Chain: "V" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 324 Classifications: {'peptide': 81} Incomplete info: {'backbone_only': 81} Link IDs: {'TRANS': 80} Chain breaks: 3 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'UNK:plan-1': 81} Unresolved non-hydrogen planarities: 81 Chain: "W" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2333 Classifications: {'peptide': 300} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 291} Chain: "X" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 63 Classifications: {'peptide': 16} Incomplete info: {'backbone_only': 15, 'n_c_alpha_c_only': 1} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 17 Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3878 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 17, 'TRANS': 468} Chain breaks: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 93.770 77.827 171.174 1.00117.25 S ATOM 486 SG CYS A 74 94.040 81.833 171.340 1.00111.80 S ATOM 768 SG CYS A 111 137.912 73.247 190.959 1.00155.94 S ATOM 796 SG CYS A 114 136.157 73.338 194.021 1.00149.48 S ATOM 19993 SG CYS B1119 104.682 90.581 180.326 1.00107.14 S ATOM 20015 SG CYS B1122 107.724 87.632 180.162 1.00107.48 S ATOM 20130 SG CYS B1137 103.803 86.665 179.870 1.00124.23 S ATOM 21117 SG CYS C 88 69.721 93.066 107.346 1.00101.13 S ATOM 21130 SG CYS C 90 69.558 90.041 109.295 1.00103.04 S ATOM 21165 SG CYS C 94 68.876 89.726 105.847 1.00 91.83 S ATOM 21187 SG CYS C 97 72.191 88.940 107.004 1.00 92.65 S ATOM 28507 SG CYS I 17 174.209 36.643 148.392 1.00119.90 S ATOM 28531 SG CYS I 20 171.135 36.270 150.349 1.00124.94 S ATOM 28692 SG CYS I 39 172.468 39.299 151.765 1.00131.91 S ATOM 28717 SG CYS I 42 174.419 35.554 151.775 1.00130.15 S ATOM 29069 SG CYS I 86 171.718 54.991 107.256 1.00110.24 S ATOM 29093 SG CYS I 89 171.056 52.005 104.728 1.00112.38 S ATOM 29297 SG CYS I 114 167.939 54.246 106.945 1.00105.02 S ATOM 29332 SG CYS I 119 170.429 51.758 108.326 1.00107.70 S ATOM 29442 SG CYS J 7 102.229 82.680 98.765 1.00 66.18 S ATOM 29730 SG CYS J 44 104.567 85.076 96.312 1.00 71.21 S ATOM 29736 SG CYS J 45 101.894 82.821 94.464 1.00 71.33 S ATOM 30898 SG CYS L 19 86.032 47.990 120.947 1.00100.50 S ATOM 30917 SG CYS L 22 84.158 46.070 118.583 1.00100.52 S ATOM 31034 SG CYS L 36 82.721 46.279 121.901 1.00106.90 S ATOM 31060 SG CYS L 39 86.884 44.067 120.290 1.00112.55 S ATOM 45559 SG CYS Y 16 108.538 22.292 193.958 1.00364.03 S ATOM 45581 SG CYS Y 19 112.573 22.248 192.996 1.00367.84 S ATOM 45693 SG CYS Y 33 110.802 19.310 192.101 1.00370.66 S ATOM 45715 SG CYS Y 36 112.436 19.828 196.043 1.00371.23 S Residues with excluded nonbonded symmetry interactions: 94 residue: pdb=" N ASN M1145 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1145 " occ=0.00 residue: pdb=" N THR M1146 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1146 " occ=0.00 residue: pdb=" N GLU M1147 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1147 " occ=0.00 residue: pdb=" N GLU M1148 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1148 " occ=0.00 residue: pdb=" N ILE M1149 " occ=0.00 ... (2 atoms not shown) pdb=" O ILE M1149 " occ=0.00 residue: pdb=" N PHE M1150 " occ=0.00 ... (2 atoms not shown) pdb=" O PHE M1150 " occ=0.00 residue: pdb=" N ASN M1151 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1151 " occ=0.00 residue: pdb=" N MET M1152 " occ=0.00 ... (2 atoms not shown) pdb=" O MET M1152 " occ=0.00 residue: pdb=" N LEU M1153 " occ=0.00 ... (2 atoms not shown) pdb=" O LEU M1153 " occ=0.00 residue: pdb=" N THR M1154 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1154 " occ=0.00 residue: pdb=" N LYS M1155 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS M1155 " occ=0.00 residue: pdb=" N GLU M1156 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1156 " occ=0.00 ... (remaining 82 not shown) Time building chain proxies: 25.09, per 1000 atoms: 0.50 Number of scatterers: 50239 At special positions: 0 Unit cell: (207.702, 190.918, 247.564, 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 9 29.99 S 235 16.00 P 108 15.00 Mg 1 11.99 O 10082 8.00 N 9346 7.00 C 30458 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 Atom "HETATM11330 OG SEP A1547 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.82 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 36 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " Number of angles added : 30 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 238 helices and 60 sheets defined 38.2% alpha, 14.1% beta 46 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 21.31 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.737A pdb=" N LYS A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 318 removed outlier: 3.650A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 350 through 353 No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 382 through 385 No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 489 through 492 No H-bonds generated for 'chain 'A' and resid 489 through 492' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 557 through 566 removed outlier: 4.021A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.751A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.945A pdb=" N ASP A 614 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 662 through 683 removed outlier: 3.962A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 772 removed outlier: 3.745A pdb=" N MET A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 785 removed outlier: 3.804A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 868 removed outlier: 3.855A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 898 through 900 No H-bonds generated for 'chain 'A' and resid 898 through 900' Processing helix chain 'A' and resid 914 through 920 Processing helix chain 'A' and resid 927 through 933 removed outlier: 3.677A pdb=" N THR A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 944 removed outlier: 3.944A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 969 removed outlier: 3.633A pdb=" N GLU A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 993 removed outlier: 3.573A pdb=" N LYS A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1019 removed outlier: 3.745A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1037 removed outlier: 3.544A pdb=" N ALA A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1062 through 1079 removed outlier: 3.767A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1096 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1121 through 1128 Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.837A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1218 through 1224 Processing helix chain 'A' and resid 1228 through 1238 Processing helix chain 'A' and resid 1283 through 1294 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1371 through 1389 removed outlier: 3.569A pdb=" N LYS A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A1385 " --> pdb=" O GLU A1381 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1404 Processing helix chain 'A' and resid 1416 through 1419 No H-bonds generated for 'chain 'A' and resid 1416 through 1419' Processing helix chain 'A' and resid 1426 through 1431 removed outlier: 4.060A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1445 Processing helix chain 'A' and resid 1454 through 1457 No H-bonds generated for 'chain 'A' and resid 1454 through 1457' Processing helix chain 'A' and resid 1479 through 1481 No H-bonds generated for 'chain 'A' and resid 1479 through 1481' Processing helix chain 'B' and resid 22 through 36 removed outlier: 4.758A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 61 removed outlier: 5.355A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.856A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.688A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 324 removed outlier: 3.964A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 removed outlier: 3.880A pdb=" N LYS B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 376 removed outlier: 3.543A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 425 removed outlier: 3.811A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.833A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 539 through 547 removed outlier: 4.173A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 591 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 707 through 710 removed outlier: 3.788A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 730 removed outlier: 3.514A pdb=" N TYR B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 971 No H-bonds generated for 'chain 'B' and resid 969 through 971' Processing helix chain 'B' and resid 978 through 993 removed outlier: 3.631A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.801A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1096 removed outlier: 3.631A pdb=" N ASP B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1109 through 1112 No H-bonds generated for 'chain 'B' and resid 1109 through 1112' Processing helix chain 'B' and resid 1153 through 1164 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.695A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 78 through 81 No H-bonds generated for 'chain 'C' and resid 78 through 81' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 270 removed outlier: 3.874A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 70 Processing helix chain 'D' and resid 77 through 89 removed outlier: 3.836A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 removed outlier: 4.775A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 4 through 24 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 44 Processing helix chain 'E' and resid 85 through 96 removed outlier: 4.019A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 75 removed outlier: 3.710A pdb=" N LEU F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'G' and resid 15 through 18 Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 25 Processing helix chain 'J' and resid 31 through 37 removed outlier: 4.301A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.854A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.729A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.725A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 52 removed outlier: 4.372A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 112 removed outlier: 3.730A pdb=" N SER K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 290 No H-bonds generated for 'chain 'M' and resid 287 through 290' Processing helix chain 'M' and resid 296 through 299 No H-bonds generated for 'chain 'M' and resid 296 through 299' Processing helix chain 'M' and resid 311 through 323 removed outlier: 4.605A pdb=" N GLU M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 352 through 366 Processing helix chain 'M' and resid 373 through 378 Processing helix chain 'M' and resid 392 through 429 Processing helix chain 'M' and resid 446 through 452 Processing helix chain 'M' and resid 457 through 470 WARNING: missing atoms! Processing helix chain 'M' and resid 543 through 547 Processing helix chain 'M' and resid 589 through 597 Processing helix chain 'M' and resid 600 through 606 removed outlier: 3.753A pdb=" N GLN M 604 " --> pdb=" O PRO M 600 " (cutoff:3.500A) Processing helix chain 'M' and resid 645 through 649 Processing helix chain 'M' and resid 652 through 662 removed outlier: 3.765A pdb=" N CYS M 657 " --> pdb=" O LEU M 654 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU M 658 " --> pdb=" O LYS M 655 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU M 660 " --> pdb=" O CYS M 657 " (cutoff:3.500A) Processing helix chain 'M' and resid 687 through 691 removed outlier: 3.561A pdb=" N GLN M 691 " --> pdb=" O GLU M 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 687 through 691' Processing helix chain 'M' and resid 703 through 720 Processing helix chain 'M' and resid 724 through 752 Processing helix chain 'M' and resid 760 through 762 No H-bonds generated for 'chain 'M' and resid 760 through 762' Processing helix chain 'M' and resid 831 through 840 Processing helix chain 'M' and resid 855 through 869 Processing helix chain 'M' and resid 890 through 893 No H-bonds generated for 'chain 'M' and resid 890 through 893' Processing helix chain 'M' and resid 908 through 921 Processing helix chain 'M' and resid 923 through 927 Processing helix chain 'M' and resid 937 through 939 No H-bonds generated for 'chain 'M' and resid 937 through 939' Processing helix chain 'M' and resid 952 through 969 Processing helix chain 'M' and resid 986 through 988 No H-bonds generated for 'chain 'M' and resid 986 through 988' Processing helix chain 'M' and resid 994 through 1006 Processing helix chain 'M' and resid 1015 through 1019 removed outlier: 4.061A pdb=" N THR M1019 " --> pdb=" O GLN M1016 " (cutoff:3.500A) Processing helix chain 'M' and resid 1025 through 1030 Processing helix chain 'M' and resid 1052 through 1054 No H-bonds generated for 'chain 'M' and resid 1052 through 1054' Processing helix chain 'M' and resid 1063 through 1072 removed outlier: 3.896A pdb=" N LYS M1068 " --> pdb=" O GLU M1064 " (cutoff:3.500A) Processing helix chain 'M' and resid 1086 through 1094 removed outlier: 3.629A pdb=" N GLU M1091 " --> pdb=" O GLY M1087 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE M1092 " --> pdb=" O ALA M1088 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU M1093 " --> pdb=" O LEU M1089 " (cutoff:3.500A) Processing helix chain 'M' and resid 1104 through 1111 Processing helix chain 'M' and resid 1122 through 1131 Processing helix chain 'M' and resid 1147 through 1153 Processing helix chain 'M' and resid 1242 through 1245 No H-bonds generated for 'chain 'M' and resid 1242 through 1245' Processing helix chain 'M' and resid 1253 through 1255 No H-bonds generated for 'chain 'M' and resid 1253 through 1255' Processing helix chain 'M' and resid 1272 through 1274 No H-bonds generated for 'chain 'M' and resid 1272 through 1274' Processing helix chain 'M' and resid 1283 through 1285 No H-bonds generated for 'chain 'M' and resid 1283 through 1285' Processing helix chain 'M' and resid 1340 through 1349 removed outlier: 3.838A pdb=" N THR M1349 " --> pdb=" O LYS M1345 " (cutoff:3.500A) Processing helix chain 'M' and resid 1403 through 1405 No H-bonds generated for 'chain 'M' and resid 1403 through 1405' Processing helix chain 'M' and resid 1408 through 1427 removed outlier: 4.857A pdb=" N GLN M1417 " --> pdb=" O ALA M1413 " (cutoff:3.500A) Proline residue: M1418 - end of helix Processing helix chain 'M' and resid 1435 through 1438 No H-bonds generated for 'chain 'M' and resid 1435 through 1438' Processing helix chain 'M' and resid 1440 through 1453 Processing helix chain 'M' and resid 1504 through 1514 Processing helix chain 'Q' and resid 24 through 36 Processing helix chain 'Q' and resid 41 through 54 removed outlier: 3.667A pdb=" N UNK Q 50 " --> pdb=" O UNK Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 69 Processing helix chain 'Q' and resid 80 through 96 Processing helix chain 'Q' and resid 106 through 124 Processing helix chain 'Q' and resid 128 through 140 Processing helix chain 'Q' and resid 145 through 156 Processing helix chain 'Q' and resid 163 through 176 Processing helix chain 'Q' and resid 179 through 191 Processing helix chain 'Q' and resid 197 through 210 removed outlier: 4.166A pdb=" N UNK Q 202 " --> pdb=" O UNK Q 198 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N UNK Q 203 " --> pdb=" O UNK Q 199 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N UNK Q 206 " --> pdb=" O UNK Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 227 Processing helix chain 'Q' and resid 233 through 245 Processing helix chain 'Q' and resid 251 through 264 Processing helix chain 'Q' and resid 269 through 282 Processing helix chain 'Q' and resid 285 through 297 Processing helix chain 'Q' and resid 306 through 318 Processing helix chain 'Q' and resid 322 through 335 Processing helix chain 'Q' and resid 337 through 354 removed outlier: 5.625A pdb=" N VAL Q 341 " --> pdb=" O SER Q 338 " (cutoff:3.500A) Proline residue: Q 343 - end of helix removed outlier: 4.387A pdb=" N GLY Q 348 " --> pdb=" O PHE Q 345 " (cutoff:3.500A) Processing helix chain 'Q' and resid 357 through 370 Processing helix chain 'Q' and resid 375 through 388 Processing helix chain 'Q' and resid 391 through 407 removed outlier: 4.733A pdb=" N ILE Q 396 " --> pdb=" O GLU Q 392 " (cutoff:3.500A) Processing helix chain 'Q' and resid 412 through 424 Processing helix chain 'Q' and resid 430 through 447 removed outlier: 4.037A pdb=" N ILE Q 440 " --> pdb=" O THR Q 436 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU Q 443 " --> pdb=" O ARG Q 439 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) Processing helix chain 'Q' and resid 451 through 464 Processing helix chain 'Q' and resid 467 through 479 removed outlier: 3.557A pdb=" N LEU Q 478 " --> pdb=" O PHE Q 474 " (cutoff:3.500A) Processing helix chain 'Q' and resid 482 through 485 No H-bonds generated for 'chain 'Q' and resid 482 through 485' Processing helix chain 'Q' and resid 491 through 509 removed outlier: 6.199A pdb=" N ILE Q 495 " --> pdb=" O TYR Q 492 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER Q 496 " --> pdb=" O ASN Q 493 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL Q 497 " --> pdb=" O ALA Q 494 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR Q 498 " --> pdb=" O ILE Q 495 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU Q 503 " --> pdb=" O SER Q 500 " (cutoff:3.500A) Processing helix chain 'Q' and resid 513 through 526 Processing helix chain 'Q' and resid 531 through 543 Processing helix chain 'Q' and resid 547 through 560 Processing helix chain 'Q' and resid 565 through 577 Processing helix chain 'Q' and resid 581 through 591 Processing helix chain 'Q' and resid 601 through 615 removed outlier: 3.624A pdb=" N THR Q 614 " --> pdb=" O VAL Q 610 " (cutoff:3.500A) Processing helix chain 'Q' and resid 618 through 626 removed outlier: 3.975A pdb=" N ASP Q 621 " --> pdb=" O PRO Q 618 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU Q 623 " --> pdb=" O ARG Q 620 " (cutoff:3.500A) Processing helix chain 'Q' and resid 628 through 640 Processing helix chain 'Q' and resid 647 through 659 Processing helix chain 'Q' and resid 661 through 675 removed outlier: 4.527A pdb=" N ARG Q 664 " --> pdb=" O GLY Q 661 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG Q 667 " --> pdb=" O ARG Q 664 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL Q 673 " --> pdb=" O PHE Q 670 " (cutoff:3.500A) Processing helix chain 'Q' and resid 681 through 693 Processing helix chain 'Q' and resid 697 through 711 Processing helix chain 'Q' and resid 719 through 727 removed outlier: 3.772A pdb=" N ALA Q 726 " --> pdb=" O TYR Q 722 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU Q 727 " --> pdb=" O LEU Q 723 " (cutoff:3.500A) Processing helix chain 'Q' and resid 739 through 743 Processing helix chain 'Q' and resid 756 through 772 removed outlier: 4.098A pdb=" N ALA Q 765 " --> pdb=" O LEU Q 761 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP Q 771 " --> pdb=" O SER Q 767 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU Q 772 " --> pdb=" O VAL Q 768 " (cutoff:3.500A) Processing helix chain 'Q' and resid 779 through 796 removed outlier: 3.817A pdb=" N TYR Q 795 " --> pdb=" O ARG Q 791 " (cutoff:3.500A) Processing helix chain 'Q' and resid 809 through 890 removed outlier: 3.710A pdb=" N ARG Q 815 " --> pdb=" O ALA Q 811 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER Q 818 " --> pdb=" O ALA Q 814 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR Q 826 " --> pdb=" O SER Q 822 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA Q 829 " --> pdb=" O GLN Q 825 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 395 Processing helix chain 'U' and resid 499 through 514 Processing helix chain 'V' and resid 211 through 213 No H-bonds generated for 'chain 'V' and resid 211 through 213' Processing helix chain 'X' and resid 248 through 259 Processing helix chain 'Y' and resid 3 through 5 No H-bonds generated for 'chain 'Y' and resid 3 through 5' Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 37 through 40 No H-bonds generated for 'chain 'Y' and resid 37 through 40' Processing helix chain 'Y' and resid 46 through 52 Processing helix chain 'Y' and resid 66 through 68 No H-bonds generated for 'chain 'Y' and resid 66 through 68' Processing helix chain 'Y' and resid 70 through 75 Processing helix chain 'Y' and resid 95 through 103 Processing helix chain 'Z' and resid 189 through 202 Processing helix chain 'Z' and resid 232 through 238 Processing helix chain 'Z' and resid 246 through 248 No H-bonds generated for 'chain 'Z' and resid 246 through 248' Processing helix chain 'Z' and resid 257 through 263 removed outlier: 4.679A pdb=" N THR Z 261 " --> pdb=" O LYS Z 258 " (cutoff:3.500A) Processing helix chain 'Z' and resid 342 through 348 Processing helix chain 'Z' and resid 390 through 395 Processing helix chain 'Z' and resid 465 through 467 No H-bonds generated for 'chain 'Z' and resid 465 through 467' Processing helix chain 'Z' and resid 515 through 517 No H-bonds generated for 'chain 'Z' and resid 515 through 517' Processing helix chain 'Z' and resid 631 through 634 Processing helix chain 'Z' and resid 640 through 642 No H-bonds generated for 'chain 'Z' and resid 640 through 642' Processing sheet with id= A, first strand: chain 'A' and resid 86 through 89 Processing sheet with id= B, first strand: chain 'A' and resid 190 through 194 Processing sheet with id= C, first strand: chain 'A' and resid 362 through 366 Processing sheet with id= D, first strand: chain 'A' and resid 367 through 369 removed outlier: 6.240A pdb=" N PHE A 482 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 377 through 380 removed outlier: 6.366A pdb=" N ARG A 473 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL A 380 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG A 475 " --> pdb=" O VAL A 380 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.912A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= H, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id= I, first strand: chain 'A' and resid 1245 through 1247 Processing sheet with id= J, first strand: chain 'B' and resid 87 through 89 Processing sheet with id= K, first strand: chain 'B' and resid 391 through 394 Processing sheet with id= L, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.789A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= N, first strand: chain 'B' and resid 602 through 605 removed outlier: 3.539A pdb=" N ILE B 567 " --> pdb=" O GLY B 575 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 748 through 751 removed outlier: 5.345A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 1042 through 1048 removed outlier: 4.402A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 965 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N MET B 796 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN B 948 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 827 through 829 Processing sheet with id= R, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id= S, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id= T, first strand: chain 'B' and resid 121 through 126 removed outlier: 4.089A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.513A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 99 through 106 removed outlier: 6.040A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.594A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 61 through 63 removed outlier: 7.291A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 147 through 150 Processing sheet with id= Z, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AA, first strand: chain 'G' and resid 5 through 13 removed outlier: 3.587A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 104 through 109 removed outlier: 6.156A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 118 through 120 Processing sheet with id= AD, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.416A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.729A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 25 through 29 Processing sheet with id= AG, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= AH, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AI, first strand: chain 'L' and resid 16 through 18 Processing sheet with id= AJ, first strand: chain 'M' and resid 882 through 884 removed outlier: 6.076A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASN M 800 " --> pdb=" O VAL M 805 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL M 805 " --> pdb=" O ASN M 800 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 1237 through 1240 removed outlier: 6.048A pdb=" N ARG M1231 " --> pdb=" O VAL M1171 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL M1171 " --> pdb=" O ARG M1231 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG M1266 " --> pdb=" O THR M1280 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASP M1278 " --> pdb=" O MET M1268 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE M1270 " --> pdb=" O SER M1276 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER M1276 " --> pdb=" O ILE M1270 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 1330 through 1332 removed outlier: 6.504A pdb=" N VAL M1355 " --> pdb=" O UNK M1331 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU M1367 " --> pdb=" O VAL M1383 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE M1377 " --> pdb=" O VAL M1373 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 1460 through 1464 Processing sheet with id= AN, first strand: chain 'V' and resid 321 through 325 removed outlier: 3.623A pdb=" N UNK U 374 " --> pdb=" O UNK V 314 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N UNK V 316 " --> pdb=" O UNK U 372 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N UNK U 372 " --> pdb=" O UNK V 316 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N UNK U 484 " --> pdb=" O UNK U 373 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N UNK U 375 " --> pdb=" O UNK U 484 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N UNK U 486 " --> pdb=" O UNK U 375 " (cutoff:3.500A) removed outlier: 12.725A pdb=" N UNK U 377 " --> pdb=" O UNK U 486 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N UNK U 488 " --> pdb=" O UNK U 377 " (cutoff:3.500A) removed outlier: 13.648A pdb=" N UNK U 379 " --> pdb=" O UNK U 488 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N UNK U 490 " --> pdb=" O UNK U 379 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N UNK U 488 " --> pdb=" O UNK U 462 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'U' and resid 449 through 451 Processing sheet with id= AP, first strand: chain 'U' and resid 479 through 481 removed outlier: 3.591A pdb=" N UNK U 472 " --> pdb=" O UNK V 201 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N UNK V 201 " --> pdb=" O UNK U 472 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N UNK U 474 " --> pdb=" O UNK V 199 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N UNK V 199 " --> pdb=" O UNK U 474 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N UNK V 328 " --> pdb=" O UNK V 202 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N UNK V 204 " --> pdb=" O UNK V 328 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N UNK V 330 " --> pdb=" O UNK V 204 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'W' and resid 19 through 24 removed outlier: 6.767A pdb=" N GLY W 38 " --> pdb=" O TRP W 20 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL W 22 " --> pdb=" O VAL W 36 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL W 36 " --> pdb=" O VAL W 22 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP W 24 " --> pdb=" O THR W 34 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR W 34 " --> pdb=" O TRP W 24 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS W 48 " --> pdb=" O LEU W 56 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU W 56 " --> pdb=" O LYS W 48 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG W 50 " --> pdb=" O LEU W 54 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU W 54 " --> pdb=" O ARG W 50 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'W' and resid 67 through 72 removed outlier: 7.034A pdb=" N SER W 82 " --> pdb=" O VAL W 68 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL W 70 " --> pdb=" O ALA W 80 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA W 80 " --> pdb=" O VAL W 70 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE W 72 " --> pdb=" O ILE W 78 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE W 78 " --> pdb=" O ILE W 72 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER W 83 " --> pdb=" O HIS W 87 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS W 100 " --> pdb=" O LEU W 90 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASP W 92 " --> pdb=" O GLN W 98 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN W 98 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'W' and resid 112 through 114 removed outlier: 6.094A pdb=" N GLY W 134 " --> pdb=" O LYS W 140 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS W 140 " --> pdb=" O GLY W 134 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'W' and resid 151 through 156 removed outlier: 6.877A pdb=" N GLY W 166 " --> pdb=" O LEU W 152 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE W 154 " --> pdb=" O ALA W 164 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA W 164 " --> pdb=" O ILE W 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR W 156 " --> pdb=" O TYR W 162 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR W 162 " --> pdb=" O TYR W 156 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP W 176 " --> pdb=" O LEU W 182 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU W 182 " --> pdb=" O ASP W 176 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'W' and resid 193 through 198 removed outlier: 7.038A pdb=" N ALA W 208 " --> pdb=" O ARG W 194 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU W 196 " --> pdb=" O VAL W 206 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL W 206 " --> pdb=" O LEU W 196 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE W 198 " --> pdb=" O LEU W 204 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU W 204 " --> pdb=" O PHE W 198 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASP W 218 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU W 224 " --> pdb=" O ASP W 218 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'W' and resid 235 through 240 removed outlier: 6.830A pdb=" N SER W 250 " --> pdb=" O LEU W 236 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL W 238 " --> pdb=" O VAL W 248 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL W 248 " --> pdb=" O VAL W 238 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE W 240 " --> pdb=" O HIS W 246 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N HIS W 246 " --> pdb=" O PHE W 240 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER W 255 " --> pdb=" O SER W 251 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS W 268 " --> pdb=" O VAL W 258 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP W 260 " --> pdb=" O CYS W 266 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N CYS W 266 " --> pdb=" O ASP W 260 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'W' and resid 6 through 11 removed outlier: 3.815A pdb=" N GLY W 6 " --> pdb=" O ASP W 302 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE W 300 " --> pdb=" O LEU W 8 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS W 10 " --> pdb=" O ILE W 298 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE W 298 " --> pdb=" O LYS W 10 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id= AY, first strand: chain 'Y' and resid 61 through 63 Processing sheet with id= AZ, first strand: chain 'Z' and resid 178 through 183 removed outlier: 3.662A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Z' and resid 278 through 280 removed outlier: 6.527A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Z' and resid 352 through 355 removed outlier: 3.995A pdb=" N PHE Z 358 " --> pdb=" O ASP Z 355 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'Z' and resid 425 through 427 Processing sheet with id= BD, first strand: chain 'Z' and resid 518 through 520 removed outlier: 7.176A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'Z' and resid 539 through 541 removed outlier: 6.613A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'Z' and resid 585 through 587 Processing sheet with id= BG, first strand: chain 'Z' and resid 643 through 645 removed outlier: 6.872A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Z' and resid 750 through 752 removed outlier: 6.661A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) 1903 hydrogen bonds defined for protein. 5406 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 122 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 23.93 Time building geometry restraints manager: 20.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15182 1.33 - 1.46: 9753 1.46 - 1.58: 25735 1.58 - 1.70: 215 1.70 - 1.82: 371 Bond restraints: 51256 Sorted by residual: bond pdb=" OG1 TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.717 1.601 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" O1P TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.525 1.606 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" O3P TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C CYS D 104 " pdb=" N PRO D 105 " ideal model delta sigma weight residual 1.332 1.371 -0.039 1.26e-02 6.30e+03 9.77e+00 bond pdb=" CA GLU B 70 " pdb=" CB GLU B 70 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.27e-02 6.20e+03 8.89e+00 ... (remaining 51251 not shown) Histogram of bond angle deviations from ideal: 94.92 - 103.17: 586 103.17 - 111.42: 19479 111.42 - 119.67: 22564 119.67 - 127.92: 25783 127.92 - 136.17: 539 Bond angle restraints: 68951 Sorted by residual: angle pdb=" C THR E 56 " pdb=" N ASP E 57 " pdb=" CA ASP E 57 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.85e+01 angle pdb=" C PHE A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" N ASP M1082 " pdb=" CA ASP M1082 " pdb=" C ASP M1082 " ideal model delta sigma weight residual 113.18 105.43 7.75 1.33e+00 5.65e-01 3.40e+01 angle pdb=" CA ASP Z 543 " pdb=" C ASP Z 543 " pdb=" N PRO Z 544 " ideal model delta sigma weight residual 117.68 121.76 -4.08 7.10e-01 1.98e+00 3.30e+01 angle pdb=" C ALA I 104 " pdb=" N GLU I 105 " pdb=" CA GLU I 105 " ideal model delta sigma weight residual 120.82 129.10 -8.28 1.50e+00 4.44e-01 3.05e+01 ... (remaining 68946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 27791 35.27 - 70.54: 626 70.54 - 105.81: 35 105.81 - 141.08: 0 141.08 - 176.34: 5 Dihedral angle restraints: 28457 sinusoidal: 11792 harmonic: 16665 Sorted by residual: dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N TRP B 99 " pdb=" CA TRP B 99 " ideal model delta harmonic sigma weight residual 180.00 135.34 44.66 0 5.00e+00 4.00e-02 7.98e+01 dihedral pdb=" CA GLU B 629 " pdb=" C GLU B 629 " pdb=" N LYS B 630 " pdb=" CA LYS B 630 " ideal model delta harmonic sigma weight residual -180.00 -135.60 -44.40 0 5.00e+00 4.00e-02 7.89e+01 dihedral pdb=" CA GLU C 91 " pdb=" C GLU C 91 " pdb=" N GLU C 92 " pdb=" CA GLU C 92 " ideal model delta harmonic sigma weight residual -180.00 -139.09 -40.91 0 5.00e+00 4.00e-02 6.69e+01 ... (remaining 28454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5938 0.094 - 0.189: 734 0.189 - 0.283: 40 0.283 - 0.377: 8 0.377 - 0.471: 3 Chirality restraints: 6723 Sorted by residual: chirality pdb=" CB ILE A 65 " pdb=" CA ILE A 65 " pdb=" CG1 ILE A 65 " pdb=" CG2 ILE A 65 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CG LEU A 760 " pdb=" CB LEU A 760 " pdb=" CD1 LEU A 760 " pdb=" CD2 LEU A 760 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 6720 not shown) Planarity restraints: 9154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M1515 " -0.006 2.00e-02 2.50e+03 3.65e-02 2.67e+01 pdb=" CG TYR M1515 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR M1515 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR M1515 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR M1515 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR M1515 " -0.042 2.00e-02 2.50e+03 pdb=" CZ TYR M1515 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR M1515 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1540 " 0.062 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO A1541 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A1541 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A1541 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 573 " 0.018 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP B 573 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 573 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 573 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 573 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 573 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 573 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 573 " -0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 573 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 573 " 0.010 2.00e-02 2.50e+03 ... (remaining 9151 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 193 2.52 - 3.11: 35382 3.11 - 3.71: 75364 3.71 - 4.30: 107266 4.30 - 4.90: 173367 Nonbonded interactions: 391572 Sorted by model distance: nonbonded pdb=" NZ LYS E 85 " pdb=" OP2 DC N 41 " model vdw 1.921 2.520 nonbonded pdb=" OE2 GLU B 816 " pdb=" NZ LYS B 869 " model vdw 2.002 2.520 nonbonded pdb=" O LEU I 65 " pdb=" NH1 ARG I 122 " model vdw 2.062 2.520 nonbonded pdb=" O3' U P 46 " pdb="MG MG A2003 " model vdw 2.084 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 2.110 2.170 ... (remaining 391567 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 2.590 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: 0.060 Extract box with map and model: 12.360 Check model and map are aligned: 0.810 Set scattering table: 0.500 Process input model: 142.240 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.006 0.116 51256 Z= 0.425 Angle : 0.973 14.789 68951 Z= 0.540 Chirality : 0.061 0.471 6723 Planarity : 0.006 0.095 9154 Dihedral : 13.097 176.344 18817 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 0.53 % Allowed : 4.71 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.09), residues: 6303 helix: -1.97 (0.08), residues: 2289 sheet: -1.20 (0.17), residues: 817 loop : -1.99 (0.10), residues: 3197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP B 573 HIS 0.014 0.002 HIS A 809 PHE 0.049 0.004 PHE G 44 TYR 0.073 0.003 TYR M1515 ARG 0.013 0.001 ARG B1131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 742 time to evaluate : 5.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.7711 (t-170) cc_final: 0.7510 (t-90) REVERT: A 309 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9127 (tm) REVERT: A 327 ARG cc_start: 0.8883 (mpt90) cc_final: 0.8631 (mmt-90) REVERT: A 425 ASP cc_start: 0.8091 (m-30) cc_final: 0.7649 (m-30) REVERT: A 467 MET cc_start: 0.8647 (mpt) cc_final: 0.8256 (mpp) REVERT: A 495 ASP cc_start: 0.7390 (t0) cc_final: 0.5899 (t0) REVERT: A 655 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9471 (mp) REVERT: A 750 ASP cc_start: 0.8310 (m-30) cc_final: 0.8040 (m-30) REVERT: A 1359 SER cc_start: 0.8847 (p) cc_final: 0.8569 (t) REVERT: B 792 ASP cc_start: 0.7914 (m-30) cc_final: 0.7553 (m-30) REVERT: B 1081 ASP cc_start: 0.8486 (t70) cc_final: 0.8088 (t0) REVERT: D 16 ASP cc_start: 0.8254 (t0) cc_final: 0.8036 (t70) REVERT: D 38 HIS cc_start: 0.9487 (t70) cc_final: 0.9195 (t-90) REVERT: D 44 ARG cc_start: 0.8807 (ttt-90) cc_final: 0.8521 (tpt90) REVERT: D 62 MET cc_start: 0.8894 (mmp) cc_final: 0.8665 (mmp) REVERT: D 70 ARG cc_start: 0.7998 (mtp180) cc_final: 0.7459 (ptm160) REVERT: F 57 MET cc_start: 0.9145 (ttp) cc_final: 0.8899 (ttp) REVERT: G 2 PHE cc_start: 0.7916 (m-80) cc_final: 0.7657 (m-10) REVERT: G 4 HIS cc_start: 0.8027 (t-170) cc_final: 0.7592 (t70) REVERT: G 24 ASN cc_start: 0.8964 (t0) cc_final: 0.8573 (t0) REVERT: G 28 GLN cc_start: 0.8604 (mp10) cc_final: 0.7899 (mp10) REVERT: G 48 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8595 (m) REVERT: G 98 PHE cc_start: 0.8535 (m-10) cc_final: 0.8297 (m-80) REVERT: G 104 MET cc_start: 0.7245 (ttp) cc_final: 0.6762 (tmm) REVERT: G 142 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7276 (mm-30) REVERT: H 13 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8734 (mmmt) REVERT: H 118 TYR cc_start: 0.9064 (m-80) cc_final: 0.8450 (m-80) REVERT: H 128 ASP cc_start: 0.8103 (p0) cc_final: 0.7781 (p0) REVERT: K 38 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7994 (mm-30) REVERT: K 80 ASP cc_start: 0.8229 (p0) cc_final: 0.8018 (p0) REVERT: Q 762 GLN cc_start: 0.5640 (mt0) cc_final: 0.5214 (mm-40) REVERT: Q 823 GLN cc_start: 0.3462 (mt0) cc_final: 0.3198 (tm-30) REVERT: Q 871 GLN cc_start: 0.9376 (mm-40) cc_final: 0.9131 (pp30) REVERT: Q 872 LYS cc_start: 0.8938 (tptt) cc_final: 0.8474 (ptmm) REVERT: Q 878 ARG cc_start: 0.7784 (tpt170) cc_final: 0.7098 (tpt-90) REVERT: Z 254 MET cc_start: 0.8818 (ttp) cc_final: 0.8561 (tpp) REVERT: Z 378 MET cc_start: -0.2982 (mtt) cc_final: -0.3463 (mtp) REVERT: Z 597 LYS cc_start: 0.6333 (mttt) cc_final: 0.6063 (mtmt) outliers start: 24 outliers final: 7 residues processed: 764 average time/residue: 0.6702 time to fit residues: 817.4134 Evaluate side-chains 449 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 439 time to evaluate : 5.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain Q residue 776 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 510 optimal weight: 50.0000 chunk 457 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 473 optimal weight: 50.0000 chunk 183 optimal weight: 0.9990 chunk 287 optimal weight: 10.0000 chunk 352 optimal weight: 2.9990 chunk 548 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 620 HIS A 678 ASN A 757 GLN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 HIS A1093 GLN A1108 HIS ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN A1220 HIS A1248 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 525 ASN B 631 GLN B 649 ASN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN H 130 ASN I 22 ASN I 56 ASN I 60 HIS I 84 HIS M1365 ASN M1379 GLN Q 756 ASN Q 775 ASN Q 834 GLN Q 877 GLN W 98 GLN W 189 HIS W 221 HIS ** W 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 273 HIS Y 12 HIS ** Z 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 51256 Z= 0.379 Angle : 0.663 13.376 68951 Z= 0.346 Chirality : 0.046 0.218 6723 Planarity : 0.004 0.093 9154 Dihedral : 13.710 178.680 8573 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 1.80 % Allowed : 9.06 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.10), residues: 6303 helix: -0.33 (0.10), residues: 2285 sheet: -1.17 (0.17), residues: 871 loop : -1.58 (0.10), residues: 3147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 988 HIS 0.008 0.001 HIS I 84 PHE 0.038 0.002 PHE D 26 TYR 0.029 0.002 TYR G 3 ARG 0.011 0.001 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 472 time to evaluate : 5.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.7793 (t-170) cc_final: 0.7560 (t-170) REVERT: A 309 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9240 (tm) REVERT: A 495 ASP cc_start: 0.7502 (t0) cc_final: 0.6737 (t0) REVERT: A 750 ASP cc_start: 0.8347 (m-30) cc_final: 0.8110 (m-30) REVERT: A 1296 MET cc_start: 0.8622 (mmm) cc_final: 0.8406 (mmm) REVERT: A 1359 SER cc_start: 0.8903 (p) cc_final: 0.8396 (t) REVERT: B 198 GLU cc_start: 0.7739 (pt0) cc_final: 0.6774 (pt0) REVERT: B 671 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7739 (mt-10) REVERT: B 792 ASP cc_start: 0.8137 (m-30) cc_final: 0.7937 (m-30) REVERT: B 1081 ASP cc_start: 0.8555 (t70) cc_final: 0.8125 (t0) REVERT: D 38 HIS cc_start: 0.9486 (t70) cc_final: 0.9182 (t70) REVERT: D 62 MET cc_start: 0.8930 (mmp) cc_final: 0.8595 (mmm) REVERT: G 2 PHE cc_start: 0.8183 (m-80) cc_final: 0.7290 (m-80) REVERT: G 44 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8703 (m-80) REVERT: G 104 MET cc_start: 0.7288 (ttp) cc_final: 0.6475 (tmm) REVERT: G 115 SER cc_start: 0.7446 (p) cc_final: 0.7197 (p) REVERT: G 117 MET cc_start: 0.7593 (mmm) cc_final: 0.7135 (mmm) REVERT: H 13 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8863 (mmmt) REVERT: L 25 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8011 (tt0) REVERT: W 98 GLN cc_start: 0.1399 (tt0) cc_final: 0.0935 (tp40) REVERT: Y 63 MET cc_start: 0.5760 (tmm) cc_final: 0.5459 (tmm) REVERT: Y 64 MET cc_start: 0.7056 (mtp) cc_final: 0.6613 (mtm) REVERT: Z 197 MET cc_start: 0.8579 (ttt) cc_final: 0.7599 (tpt) REVERT: Z 254 MET cc_start: 0.8861 (ttp) cc_final: 0.8565 (tpp) REVERT: Z 378 MET cc_start: -0.2934 (mtt) cc_final: -0.3411 (mtp) REVERT: Z 451 MET cc_start: 0.6064 (mmm) cc_final: 0.5849 (mmm) REVERT: Z 474 MET cc_start: 0.6690 (mpp) cc_final: 0.6467 (mmp) REVERT: Z 486 GLU cc_start: 0.8371 (pt0) cc_final: 0.7873 (pm20) REVERT: Z 508 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6534 (tpp) REVERT: Z 748 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8363 (mm-40) outliers start: 81 outliers final: 41 residues processed: 534 average time/residue: 0.6204 time to fit residues: 545.4999 Evaluate side-chains 456 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 412 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain M residue 1355 VAL Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 508 MET Chi-restraints excluded: chain Z residue 601 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 0.0970 chunk 170 optimal weight: 4.9990 chunk 456 optimal weight: 7.9990 chunk 373 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 549 optimal weight: 20.0000 chunk 593 optimal weight: 30.0000 chunk 489 optimal weight: 50.0000 chunk 544 optimal weight: 50.0000 chunk 187 optimal weight: 0.3980 chunk 440 optimal weight: 7.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1457 ASN A1462 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 130 ASN I 56 ASN I 60 HIS M1379 GLN Q 756 ASN W 11 GLN W 184 HIS Z 232 GLN ** Z 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 572 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 51256 Z= 0.338 Angle : 0.609 13.422 68951 Z= 0.317 Chirality : 0.045 0.214 6723 Planarity : 0.004 0.070 9154 Dihedral : 13.460 178.199 8570 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 2.38 % Allowed : 10.08 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.10), residues: 6303 helix: 0.53 (0.11), residues: 2283 sheet: -1.06 (0.16), residues: 894 loop : -1.31 (0.11), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1210 HIS 0.006 0.001 HIS G 4 PHE 0.031 0.002 PHE D 26 TYR 0.020 0.002 TYR B 388 ARG 0.006 0.001 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 438 time to evaluate : 5.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.8511 (tp-100) cc_final: 0.8261 (tm-30) REVERT: A 265 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7899 (t) REVERT: A 266 MET cc_start: 0.5496 (ttp) cc_final: 0.5114 (ppp) REVERT: A 301 HIS cc_start: 0.7848 (t70) cc_final: 0.7566 (t-170) REVERT: A 309 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9264 (tm) REVERT: A 343 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9002 (pp) REVERT: A 495 ASP cc_start: 0.7694 (t0) cc_final: 0.6861 (t0) REVERT: A 655 ILE cc_start: 0.9758 (OUTLIER) cc_final: 0.9456 (mp) REVERT: A 1221 MET cc_start: 0.8262 (mmm) cc_final: 0.7875 (mmm) REVERT: A 1359 SER cc_start: 0.8825 (p) cc_final: 0.8588 (t) REVERT: B 124 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9063 (pt) REVERT: B 198 GLU cc_start: 0.7500 (pt0) cc_final: 0.7087 (pt0) REVERT: B 792 ASP cc_start: 0.8182 (m-30) cc_final: 0.7930 (m-30) REVERT: B 1081 ASP cc_start: 0.8627 (t70) cc_final: 0.8240 (t0) REVERT: D 26 PHE cc_start: 0.6789 (t80) cc_final: 0.5965 (t80) REVERT: D 38 HIS cc_start: 0.9455 (t70) cc_final: 0.9167 (t-90) REVERT: D 62 MET cc_start: 0.8854 (mmp) cc_final: 0.8459 (mmm) REVERT: D 84 ARG cc_start: 0.9110 (mmt90) cc_final: 0.8861 (mmt180) REVERT: F 84 GLU cc_start: 0.8715 (mp0) cc_final: 0.8410 (mp0) REVERT: G 2 PHE cc_start: 0.7814 (m-80) cc_final: 0.7370 (m-10) REVERT: G 44 PHE cc_start: 0.8981 (t80) cc_final: 0.8553 (m-80) REVERT: G 63 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7741 (mtp180) REVERT: G 68 TYR cc_start: 0.8937 (m-80) cc_final: 0.8579 (m-80) REVERT: G 80 PHE cc_start: 0.4561 (OUTLIER) cc_final: 0.4356 (m-80) REVERT: G 86 ASP cc_start: 0.5162 (OUTLIER) cc_final: 0.4657 (p0) REVERT: G 104 MET cc_start: 0.7135 (ttp) cc_final: 0.6436 (tmm) REVERT: G 110 ARG cc_start: 0.5198 (tpt170) cc_final: 0.4967 (tpt170) REVERT: G 118 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8770 (mm-30) REVERT: G 142 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7832 (mm-30) REVERT: H 9 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9214 (mp) REVERT: H 13 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8853 (mmmm) REVERT: H 118 TYR cc_start: 0.9144 (m-80) cc_final: 0.8944 (m-80) REVERT: I 23 MET cc_start: 0.8423 (ttp) cc_final: 0.8220 (ttp) REVERT: L 44 MET cc_start: 0.8646 (mmt) cc_final: 0.8190 (mmt) REVERT: W 11 GLN cc_start: 0.7091 (tp40) cc_final: 0.6562 (mp10) REVERT: W 98 GLN cc_start: 0.1602 (tt0) cc_final: 0.1083 (tp40) REVERT: Y 63 MET cc_start: 0.6247 (tmm) cc_final: 0.5999 (tmm) REVERT: Y 64 MET cc_start: 0.7096 (mtp) cc_final: 0.6607 (mtm) REVERT: Z 197 MET cc_start: 0.8599 (ttt) cc_final: 0.7620 (tpt) REVERT: Z 254 MET cc_start: 0.8888 (ttp) cc_final: 0.8579 (tpp) REVERT: Z 378 MET cc_start: -0.3099 (mtt) cc_final: -0.3534 (mtp) REVERT: Z 486 GLU cc_start: 0.8672 (pt0) cc_final: 0.8107 (pm20) outliers start: 107 outliers final: 54 residues processed: 527 average time/residue: 0.5875 time to fit residues: 519.1600 Evaluate side-chains 468 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 406 time to evaluate : 5.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain M residue 1355 VAL Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain Q residue 776 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 542 optimal weight: 50.0000 chunk 413 optimal weight: 30.0000 chunk 285 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 262 optimal weight: 0.9980 chunk 368 optimal weight: 0.7980 chunk 551 optimal weight: 50.0000 chunk 583 optimal weight: 3.9990 chunk 288 optimal weight: 7.9990 chunk 522 optimal weight: 30.0000 chunk 157 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 144 HIS B 319 ASN B 649 ASN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS ** G 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1365 ASN ** W 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 244 ASN ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 51256 Z= 0.219 Angle : 0.561 11.944 68951 Z= 0.289 Chirality : 0.043 0.214 6723 Planarity : 0.003 0.062 9154 Dihedral : 13.332 177.669 8570 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 2.18 % Allowed : 10.86 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.11), residues: 6303 helix: 0.98 (0.11), residues: 2283 sheet: -0.85 (0.17), residues: 895 loop : -1.20 (0.11), residues: 3125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 99 HIS 0.007 0.001 HIS B 98 PHE 0.030 0.002 PHE D 26 TYR 0.014 0.001 TYR B 766 ARG 0.005 0.000 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 432 time to evaluate : 5.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.5664 (ttp) cc_final: 0.5378 (ppp) REVERT: A 301 HIS cc_start: 0.7925 (t70) cc_final: 0.7614 (t-170) REVERT: A 309 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9285 (tm) REVERT: A 343 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8916 (pp) REVERT: A 655 ILE cc_start: 0.9750 (OUTLIER) cc_final: 0.9445 (mp) REVERT: A 1221 MET cc_start: 0.8199 (mmm) cc_final: 0.7851 (mmm) REVERT: B 124 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8988 (pt) REVERT: B 1081 ASP cc_start: 0.8665 (t70) cc_final: 0.8262 (t0) REVERT: D 26 PHE cc_start: 0.6809 (t80) cc_final: 0.6215 (t80) REVERT: D 38 HIS cc_start: 0.9461 (t70) cc_final: 0.9154 (t70) REVERT: D 62 MET cc_start: 0.8761 (mmp) cc_final: 0.8333 (mmm) REVERT: F 84 GLU cc_start: 0.8803 (mp0) cc_final: 0.8447 (mp0) REVERT: F 86 GLU cc_start: 0.7721 (pm20) cc_final: 0.7475 (pm20) REVERT: G 2 PHE cc_start: 0.7787 (m-80) cc_final: 0.7245 (m-80) REVERT: G 28 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8369 (tm-30) REVERT: G 44 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: G 63 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7650 (mtp180) REVERT: G 68 TYR cc_start: 0.8938 (m-80) cc_final: 0.8674 (m-80) REVERT: G 80 PHE cc_start: 0.4155 (OUTLIER) cc_final: 0.3814 (m-80) REVERT: G 86 ASP cc_start: 0.5100 (OUTLIER) cc_final: 0.4623 (p0) REVERT: G 104 MET cc_start: 0.7107 (ttp) cc_final: 0.6497 (tmm) REVERT: G 118 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8755 (mm-30) REVERT: G 142 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7763 (mm-30) REVERT: H 13 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8843 (mmmm) REVERT: H 118 TYR cc_start: 0.9224 (m-80) cc_final: 0.8891 (m-80) REVERT: L 44 MET cc_start: 0.8657 (mmt) cc_final: 0.8084 (mmt) REVERT: M 1347 MET cc_start: -0.3127 (ptt) cc_final: -0.4619 (mtt) REVERT: M 1350 MET cc_start: 0.3447 (OUTLIER) cc_final: 0.3017 (ppp) REVERT: Q 830 ARG cc_start: -0.1228 (ttt180) cc_final: -0.1510 (ptp-170) REVERT: W 11 GLN cc_start: 0.6991 (tp40) cc_final: 0.6443 (mp10) REVERT: W 98 GLN cc_start: 0.1654 (tt0) cc_final: 0.1125 (tp40) REVERT: Y 63 MET cc_start: 0.6254 (tmm) cc_final: 0.6013 (tmm) REVERT: Y 64 MET cc_start: 0.7120 (mtp) cc_final: 0.6635 (mtm) REVERT: Z 197 MET cc_start: 0.8571 (ttt) cc_final: 0.7590 (tpt) REVERT: Z 254 MET cc_start: 0.8876 (ttp) cc_final: 0.8550 (tpp) REVERT: Z 378 MET cc_start: -0.3111 (mtt) cc_final: -0.3502 (mtp) REVERT: Z 474 MET cc_start: 0.6762 (mmm) cc_final: 0.6433 (mmp) REVERT: Z 486 GLU cc_start: 0.8754 (pt0) cc_final: 0.8248 (pm20) outliers start: 98 outliers final: 52 residues processed: 509 average time/residue: 0.5951 time to fit residues: 511.0124 Evaluate side-chains 469 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 409 time to evaluate : 5.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1303 GLN Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1355 VAL Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain Q residue 776 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 486 optimal weight: 40.0000 chunk 331 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 434 optimal weight: 50.0000 chunk 240 optimal weight: 0.6980 chunk 498 optimal weight: 50.0000 chunk 403 optimal weight: 50.0000 chunk 0 optimal weight: 7.9990 chunk 298 optimal weight: 2.9990 chunk 524 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 625 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 51256 Z= 0.381 Angle : 0.608 12.808 68951 Z= 0.313 Chirality : 0.045 0.214 6723 Planarity : 0.004 0.057 9154 Dihedral : 13.283 176.160 8568 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 2.58 % Allowed : 11.57 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 6303 helix: 1.18 (0.11), residues: 2296 sheet: -0.82 (0.16), residues: 921 loop : -1.16 (0.11), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 99 HIS 0.008 0.001 HIS B 98 PHE 0.029 0.002 PHE D 26 TYR 0.017 0.002 TYR E 26 ARG 0.005 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 408 time to evaluate : 6.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8260 (mpp80) cc_final: 0.7677 (mmm-85) REVERT: A 301 HIS cc_start: 0.8043 (t70) cc_final: 0.7683 (t-170) REVERT: A 309 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9352 (tm) REVERT: A 329 MET cc_start: 0.8819 (mtp) cc_final: 0.8573 (mtp) REVERT: A 343 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8992 (pp) REVERT: A 655 ILE cc_start: 0.9755 (OUTLIER) cc_final: 0.9460 (mp) REVERT: A 861 GLN cc_start: 0.8705 (tp40) cc_final: 0.8486 (tp-100) REVERT: A 1221 MET cc_start: 0.8325 (mmm) cc_final: 0.8015 (mmm) REVERT: A 1359 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8113 (t) REVERT: B 124 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9204 (pt) REVERT: B 1081 ASP cc_start: 0.8710 (t70) cc_final: 0.8311 (t0) REVERT: C 62 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7960 (mp0) REVERT: D 26 PHE cc_start: 0.6798 (t80) cc_final: 0.5802 (t80) REVERT: D 38 HIS cc_start: 0.9452 (t70) cc_final: 0.9127 (t70) REVERT: D 62 MET cc_start: 0.8810 (mmp) cc_final: 0.8382 (mmm) REVERT: D 74 PHE cc_start: 0.5329 (OUTLIER) cc_final: 0.4778 (p90) REVERT: F 88 ASP cc_start: 0.8736 (t0) cc_final: 0.8427 (t0) REVERT: G 2 PHE cc_start: 0.7994 (m-80) cc_final: 0.7584 (m-80) REVERT: G 28 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8405 (tm-30) REVERT: G 44 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8528 (t80) REVERT: G 63 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7671 (mtm110) REVERT: G 80 PHE cc_start: 0.4007 (OUTLIER) cc_final: 0.3399 (m-80) REVERT: G 86 ASP cc_start: 0.5542 (OUTLIER) cc_final: 0.5111 (p0) REVERT: G 98 PHE cc_start: 0.8937 (m-10) cc_final: 0.8719 (m-80) REVERT: G 104 MET cc_start: 0.7033 (ttp) cc_final: 0.6509 (tmm) REVERT: G 118 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8809 (mm-30) REVERT: G 142 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7709 (mm-30) REVERT: G 164 MET cc_start: 0.7763 (mmm) cc_final: 0.7526 (mmt) REVERT: H 9 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9163 (mp) REVERT: H 13 LYS cc_start: 0.9178 (mmmt) cc_final: 0.8697 (mmmm) REVERT: H 118 TYR cc_start: 0.9297 (m-80) cc_final: 0.8976 (m-80) REVERT: H 143 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8862 (tm) REVERT: L 44 MET cc_start: 0.8687 (mmt) cc_final: 0.8202 (mmt) REVERT: M 1347 MET cc_start: -0.3027 (ptt) cc_final: -0.4613 (mtt) REVERT: M 1350 MET cc_start: 0.3485 (OUTLIER) cc_final: 0.2998 (ppp) REVERT: Q 830 ARG cc_start: -0.1094 (ttt180) cc_final: -0.1386 (ptp-170) REVERT: W 98 GLN cc_start: 0.1746 (tt0) cc_final: 0.1199 (tp40) REVERT: Y 64 MET cc_start: 0.7215 (mtp) cc_final: 0.6654 (mtm) REVERT: Z 197 MET cc_start: 0.8587 (ttt) cc_final: 0.7593 (tpt) REVERT: Z 378 MET cc_start: -0.3131 (mtt) cc_final: -0.3595 (mtp) REVERT: Z 474 MET cc_start: 0.6741 (mmm) cc_final: 0.6399 (mmp) REVERT: Z 486 GLU cc_start: 0.8740 (pt0) cc_final: 0.8246 (pm20) outliers start: 116 outliers final: 70 residues processed: 501 average time/residue: 0.5925 time to fit residues: 507.5631 Evaluate side-chains 481 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 399 time to evaluate : 5.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1355 VAL Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain M residue 1519 VAL Chi-restraints excluded: chain Q residue 776 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 196 optimal weight: 0.1980 chunk 525 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 342 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 584 optimal weight: 9.9990 chunk 485 optimal weight: 50.0000 chunk 270 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 306 optimal weight: 0.0570 overall best weight: 1.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 232 GLN ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 51256 Z= 0.193 Angle : 0.548 12.632 68951 Z= 0.282 Chirality : 0.043 0.213 6723 Planarity : 0.003 0.056 9154 Dihedral : 13.201 176.089 8568 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 2.29 % Allowed : 12.46 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 6303 helix: 1.35 (0.11), residues: 2306 sheet: -0.70 (0.17), residues: 910 loop : -1.02 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1210 HIS 0.004 0.001 HIS I 84 PHE 0.028 0.001 PHE D 26 TYR 0.014 0.001 TYR E 26 ARG 0.004 0.000 ARG Q 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 411 time to evaluate : 5.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8193 (mpp80) cc_final: 0.7561 (mmm-85) REVERT: A 301 HIS cc_start: 0.8014 (t70) cc_final: 0.7689 (t-170) REVERT: A 309 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9350 (tm) REVERT: A 655 ILE cc_start: 0.9753 (OUTLIER) cc_final: 0.9441 (mp) REVERT: A 861 GLN cc_start: 0.8659 (tp40) cc_final: 0.8430 (tp-100) REVERT: A 1221 MET cc_start: 0.8264 (mmm) cc_final: 0.7955 (mmm) REVERT: B 124 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9053 (pt) REVERT: B 230 ARG cc_start: 0.7336 (mmm160) cc_final: 0.7057 (mmp80) REVERT: B 438 ARG cc_start: 0.8212 (tpp80) cc_final: 0.7717 (tpp80) REVERT: B 1081 ASP cc_start: 0.8720 (t70) cc_final: 0.8320 (t0) REVERT: D 38 HIS cc_start: 0.9432 (t70) cc_final: 0.9113 (t70) REVERT: D 62 MET cc_start: 0.8785 (mmp) cc_final: 0.8355 (mmm) REVERT: D 74 PHE cc_start: 0.5363 (OUTLIER) cc_final: 0.4786 (p90) REVERT: D 128 GLN cc_start: 0.8972 (mm110) cc_final: 0.8647 (mm110) REVERT: F 84 GLU cc_start: 0.8904 (mp0) cc_final: 0.8626 (mp0) REVERT: G 2 PHE cc_start: 0.7991 (m-80) cc_final: 0.7736 (m-80) REVERT: G 28 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8350 (tm-30) REVERT: G 35 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7937 (mm-30) REVERT: G 44 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8634 (t80) REVERT: G 63 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7566 (mtp180) REVERT: G 80 PHE cc_start: 0.3864 (OUTLIER) cc_final: 0.3226 (m-80) REVERT: G 86 ASP cc_start: 0.5577 (OUTLIER) cc_final: 0.5225 (p0) REVERT: G 98 PHE cc_start: 0.8982 (m-10) cc_final: 0.8630 (m-80) REVERT: G 104 MET cc_start: 0.7102 (ttp) cc_final: 0.6577 (tmm) REVERT: G 118 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8796 (mm-30) REVERT: G 142 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7757 (mm-30) REVERT: G 164 MET cc_start: 0.7814 (mmm) cc_final: 0.7571 (mmt) REVERT: H 9 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.9181 (mp) REVERT: H 13 LYS cc_start: 0.9162 (mmmt) cc_final: 0.8745 (mmmm) REVERT: H 143 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8743 (tm) REVERT: M 1347 MET cc_start: -0.3326 (ptt) cc_final: -0.4688 (mtt) REVERT: M 1350 MET cc_start: 0.3349 (OUTLIER) cc_final: 0.2827 (ppp) REVERT: Q 763 ARG cc_start: 0.4364 (mmm-85) cc_final: 0.4144 (mmm-85) REVERT: Q 830 ARG cc_start: -0.0948 (ttt180) cc_final: -0.1210 (ptp-170) REVERT: Q 878 ARG cc_start: 0.7746 (tpt170) cc_final: 0.7039 (tpt-90) REVERT: W 98 GLN cc_start: 0.1681 (tt0) cc_final: 0.1048 (tp40) REVERT: Y 64 MET cc_start: 0.7262 (mtp) cc_final: 0.6458 (mtm) REVERT: Z 197 MET cc_start: 0.8604 (ttt) cc_final: 0.7621 (tpt) REVERT: Z 254 MET cc_start: 0.8665 (ttm) cc_final: 0.8229 (mmm) REVERT: Z 378 MET cc_start: -0.3136 (mtt) cc_final: -0.3556 (mtp) REVERT: Z 474 MET cc_start: 0.6700 (mmm) cc_final: 0.6349 (mmp) REVERT: Z 486 GLU cc_start: 0.8692 (pt0) cc_final: 0.8353 (pm20) REVERT: Z 508 MET cc_start: 0.6907 (ttt) cc_final: 0.6099 (tpp) outliers start: 103 outliers final: 64 residues processed: 491 average time/residue: 0.5823 time to fit residues: 483.8393 Evaluate side-chains 470 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 396 time to evaluate : 5.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1355 VAL Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain M residue 1519 VAL Chi-restraints excluded: chain Q residue 776 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 563 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 332 optimal weight: 6.9990 chunk 426 optimal weight: 50.0000 chunk 330 optimal weight: 10.0000 chunk 491 optimal weight: 10.0000 chunk 326 optimal weight: 1.9990 chunk 582 optimal weight: 50.0000 chunk 364 optimal weight: 6.9990 chunk 354 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN C 66 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS L 23 HIS Q 834 GLN ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 51256 Z= 0.488 Angle : 0.654 13.266 68951 Z= 0.334 Chirality : 0.046 0.213 6723 Planarity : 0.004 0.056 9154 Dihedral : 13.212 175.333 8568 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 2.58 % Allowed : 12.95 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 6303 helix: 1.36 (0.11), residues: 2303 sheet: -0.80 (0.17), residues: 906 loop : -1.00 (0.11), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1210 HIS 0.006 0.001 HIS B 98 PHE 0.043 0.002 PHE D 26 TYR 0.022 0.002 TYR A 815 ARG 0.006 0.001 ARG B 483 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 398 time to evaluate : 5.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8325 (mpp80) cc_final: 0.7824 (mmm-85) REVERT: A 136 GLN cc_start: 0.8444 (tp-100) cc_final: 0.8100 (tm-30) REVERT: A 301 HIS cc_start: 0.8132 (t70) cc_final: 0.7660 (t-170) REVERT: A 495 ASP cc_start: 0.8059 (t0) cc_final: 0.7367 (t0) REVERT: A 655 ILE cc_start: 0.9751 (OUTLIER) cc_final: 0.9466 (mp) REVERT: A 861 GLN cc_start: 0.8706 (tp40) cc_final: 0.8462 (tp-100) REVERT: A 1221 MET cc_start: 0.8365 (mmm) cc_final: 0.8074 (mmm) REVERT: A 1359 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8259 (t) REVERT: B 124 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9205 (pt) REVERT: B 438 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7852 (tpp80) REVERT: B 1081 ASP cc_start: 0.8757 (t70) cc_final: 0.8369 (t0) REVERT: D 38 HIS cc_start: 0.9417 (t70) cc_final: 0.9082 (t70) REVERT: D 44 ARG cc_start: 0.9320 (tpt-90) cc_final: 0.8795 (tpp80) REVERT: D 62 MET cc_start: 0.8806 (mmp) cc_final: 0.8348 (mmm) REVERT: D 74 PHE cc_start: 0.5753 (OUTLIER) cc_final: 0.5096 (p90) REVERT: D 128 GLN cc_start: 0.9035 (mm110) cc_final: 0.8744 (mm110) REVERT: E 18 MET cc_start: 0.9025 (mmm) cc_final: 0.8659 (mmm) REVERT: F 84 GLU cc_start: 0.8960 (mp0) cc_final: 0.8681 (mp0) REVERT: G 1 MET cc_start: 0.8382 (pmm) cc_final: 0.8059 (pmm) REVERT: G 2 PHE cc_start: 0.8178 (m-80) cc_final: 0.7881 (m-80) REVERT: G 28 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8402 (tm-30) REVERT: G 44 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8713 (t80) REVERT: G 63 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7835 (mtp180) REVERT: G 80 PHE cc_start: 0.3744 (OUTLIER) cc_final: 0.3032 (m-80) REVERT: G 86 ASP cc_start: 0.5494 (OUTLIER) cc_final: 0.5041 (p0) REVERT: G 98 PHE cc_start: 0.8951 (m-10) cc_final: 0.8577 (m-80) REVERT: G 104 MET cc_start: 0.7029 (ttp) cc_final: 0.6557 (tmm) REVERT: G 110 ARG cc_start: 0.5445 (tpt170) cc_final: 0.5167 (tpt170) REVERT: G 118 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8849 (mm-30) REVERT: G 142 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7742 (mm-30) REVERT: G 164 MET cc_start: 0.7877 (mmm) cc_final: 0.7593 (mmt) REVERT: H 9 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9148 (mp) REVERT: H 13 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8723 (mmmm) REVERT: H 143 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8909 (tm) REVERT: I 23 MET cc_start: 0.8429 (ttp) cc_final: 0.8212 (ttp) REVERT: I 27 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8288 (pptt) REVERT: L 44 MET cc_start: 0.8705 (mmt) cc_final: 0.8181 (mmt) REVERT: M 1347 MET cc_start: -0.3340 (ptt) cc_final: -0.4811 (mtt) REVERT: M 1350 MET cc_start: 0.3249 (OUTLIER) cc_final: 0.2767 (ppp) REVERT: Q 830 ARG cc_start: -0.0962 (ttt180) cc_final: -0.1269 (ptp-170) REVERT: Q 878 ARG cc_start: 0.7713 (tpt170) cc_final: 0.6774 (tpp-160) REVERT: W 11 GLN cc_start: 0.7023 (tp40) cc_final: 0.6509 (mp-120) REVERT: W 98 GLN cc_start: 0.1409 (tt0) cc_final: 0.0812 (tp40) REVERT: Y 64 MET cc_start: 0.7263 (mtp) cc_final: 0.6462 (mtm) REVERT: Z 197 MET cc_start: 0.8606 (ttt) cc_final: 0.7672 (tpt) REVERT: Z 254 MET cc_start: 0.8593 (ttt) cc_final: 0.8170 (mmm) REVERT: Z 378 MET cc_start: -0.3136 (mtt) cc_final: -0.3603 (mtp) REVERT: Z 474 MET cc_start: 0.6661 (mmm) cc_final: 0.6306 (mmp) REVERT: Z 508 MET cc_start: 0.6916 (ttt) cc_final: 0.6228 (tpp) outliers start: 116 outliers final: 76 residues processed: 494 average time/residue: 0.5910 time to fit residues: 492.8864 Evaluate side-chains 482 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 395 time to evaluate : 5.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1355 VAL Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain M residue 1519 VAL Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 481 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 360 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 370 optimal weight: 0.9990 chunk 396 optimal weight: 50.0000 chunk 287 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 457 optimal weight: 40.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN B 72 GLN B 111 ASN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 51256 Z= 0.262 Angle : 0.574 13.803 68951 Z= 0.293 Chirality : 0.044 0.212 6723 Planarity : 0.003 0.056 9154 Dihedral : 13.166 174.963 8568 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 2.35 % Allowed : 13.19 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.11), residues: 6303 helix: 1.56 (0.11), residues: 2283 sheet: -0.72 (0.17), residues: 909 loop : -0.93 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1210 HIS 0.004 0.001 HIS B 98 PHE 0.037 0.002 PHE D 26 TYR 0.015 0.001 TYR H 118 ARG 0.004 0.000 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 412 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8269 (mpp80) cc_final: 0.7754 (mmm-85) REVERT: A 301 HIS cc_start: 0.8095 (t70) cc_final: 0.7730 (t-170) REVERT: A 322 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8675 (mm) REVERT: A 565 MET cc_start: 0.9337 (tpt) cc_final: 0.9039 (tpt) REVERT: A 655 ILE cc_start: 0.9752 (OUTLIER) cc_final: 0.9451 (mp) REVERT: A 861 GLN cc_start: 0.8643 (tp40) cc_final: 0.8390 (tp-100) REVERT: A 1221 MET cc_start: 0.8318 (mmm) cc_final: 0.8034 (mmm) REVERT: B 124 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9076 (pt) REVERT: B 240 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9011 (mm) REVERT: B 1081 ASP cc_start: 0.8743 (t70) cc_final: 0.8344 (t0) REVERT: D 26 PHE cc_start: 0.7148 (t80) cc_final: 0.6552 (t80) REVERT: D 38 HIS cc_start: 0.9417 (t70) cc_final: 0.9080 (t70) REVERT: D 62 MET cc_start: 0.8815 (mmp) cc_final: 0.8368 (mmm) REVERT: D 74 PHE cc_start: 0.5713 (OUTLIER) cc_final: 0.4990 (p90) REVERT: D 128 GLN cc_start: 0.9046 (mm110) cc_final: 0.8712 (mm110) REVERT: E 18 MET cc_start: 0.9064 (mmm) cc_final: 0.8710 (mmm) REVERT: F 84 GLU cc_start: 0.9013 (mp0) cc_final: 0.8774 (mp0) REVERT: G 1 MET cc_start: 0.8289 (pmm) cc_final: 0.7461 (pmm) REVERT: G 2 PHE cc_start: 0.8175 (m-80) cc_final: 0.7782 (m-80) REVERT: G 28 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8334 (tm-30) REVERT: G 35 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7922 (mm-30) REVERT: G 44 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8688 (t80) REVERT: G 63 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7828 (mtp180) REVERT: G 80 PHE cc_start: 0.3702 (OUTLIER) cc_final: 0.3056 (m-80) REVERT: G 86 ASP cc_start: 0.5719 (OUTLIER) cc_final: 0.5082 (p0) REVERT: G 98 PHE cc_start: 0.9064 (m-10) cc_final: 0.8724 (m-80) REVERT: G 104 MET cc_start: 0.7114 (ttp) cc_final: 0.6674 (tmm) REVERT: G 110 ARG cc_start: 0.5662 (tpt170) cc_final: 0.5382 (tpt170) REVERT: G 118 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8827 (mm-30) REVERT: G 142 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7734 (mm-30) REVERT: G 164 MET cc_start: 0.7916 (mmm) cc_final: 0.7344 (mmt) REVERT: H 9 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9194 (mp) REVERT: H 13 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8775 (mmmm) REVERT: H 143 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8796 (tm) REVERT: M 1347 MET cc_start: -0.3333 (ptt) cc_final: -0.4867 (mtt) REVERT: M 1350 MET cc_start: 0.3206 (OUTLIER) cc_final: 0.2932 (ppp) REVERT: Q 763 ARG cc_start: 0.4171 (mmm-85) cc_final: 0.3940 (mmm-85) REVERT: Q 830 ARG cc_start: -0.0950 (ttt180) cc_final: -0.1254 (ptp-170) REVERT: Q 878 ARG cc_start: 0.7688 (tpt170) cc_final: 0.6960 (tpt-90) REVERT: W 11 GLN cc_start: 0.7001 (tp40) cc_final: 0.6492 (mp-120) REVERT: W 98 GLN cc_start: 0.1496 (tt0) cc_final: 0.0882 (tp40) REVERT: Y 64 MET cc_start: 0.7288 (mtp) cc_final: 0.6537 (mtm) REVERT: Z 197 MET cc_start: 0.8666 (ttt) cc_final: 0.7752 (tpt) REVERT: Z 254 MET cc_start: 0.8657 (ttt) cc_final: 0.8161 (mmm) REVERT: Z 474 MET cc_start: 0.6567 (mmm) cc_final: 0.6229 (mmp) REVERT: Z 508 MET cc_start: 0.6812 (ttt) cc_final: 0.6016 (tpp) outliers start: 106 outliers final: 76 residues processed: 494 average time/residue: 0.5964 time to fit residues: 499.7185 Evaluate side-chains 483 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 396 time to evaluate : 6.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain M residue 1519 VAL Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 481 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 529 optimal weight: 0.3980 chunk 557 optimal weight: 0.9980 chunk 508 optimal weight: 50.0000 chunk 542 optimal weight: 50.0000 chunk 326 optimal weight: 0.0870 chunk 236 optimal weight: 0.9990 chunk 425 optimal weight: 0.0670 chunk 166 optimal weight: 2.9990 chunk 490 optimal weight: 8.9990 chunk 513 optimal weight: 50.0000 chunk 540 optimal weight: 8.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 145 GLN B 503 ASN B 585 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 51256 Z= 0.153 Angle : 0.554 13.917 68951 Z= 0.282 Chirality : 0.043 0.213 6723 Planarity : 0.003 0.054 9154 Dihedral : 13.051 174.931 8568 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 1.71 % Allowed : 13.99 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6303 helix: 1.66 (0.11), residues: 2298 sheet: -0.56 (0.17), residues: 901 loop : -0.91 (0.11), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1210 HIS 0.003 0.001 HIS K 40 PHE 0.033 0.001 PHE D 26 TYR 0.025 0.001 TYR G 3 ARG 0.006 0.000 ARG Q 866 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 437 time to evaluate : 5.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.8014 (t70) cc_final: 0.7659 (t-170) REVERT: A 309 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9326 (tm) REVERT: A 655 ILE cc_start: 0.9741 (OUTLIER) cc_final: 0.9428 (mp) REVERT: A 869 GLU cc_start: 0.8062 (pt0) cc_final: 0.7857 (pt0) REVERT: A 1221 MET cc_start: 0.8323 (mmm) cc_final: 0.8028 (mmm) REVERT: B 124 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9029 (pt) REVERT: B 1081 ASP cc_start: 0.8684 (t70) cc_final: 0.8331 (t0) REVERT: D 38 HIS cc_start: 0.9386 (t70) cc_final: 0.9076 (t70) REVERT: D 62 MET cc_start: 0.8844 (mmp) cc_final: 0.8425 (mmm) REVERT: D 74 PHE cc_start: 0.5486 (OUTLIER) cc_final: 0.4797 (p90) REVERT: D 128 GLN cc_start: 0.9041 (mm110) cc_final: 0.8729 (mm110) REVERT: E 18 MET cc_start: 0.9002 (mmm) cc_final: 0.8736 (mmm) REVERT: F 84 GLU cc_start: 0.9023 (mp0) cc_final: 0.8815 (mp0) REVERT: G 1 MET cc_start: 0.8595 (pmm) cc_final: 0.8367 (pmm) REVERT: G 2 PHE cc_start: 0.7810 (m-80) cc_final: 0.7566 (m-10) REVERT: G 44 PHE cc_start: 0.9110 (t80) cc_final: 0.8709 (t80) REVERT: G 63 ARG cc_start: 0.8193 (mtp85) cc_final: 0.7842 (mtp180) REVERT: G 80 PHE cc_start: 0.3985 (OUTLIER) cc_final: 0.3334 (m-80) REVERT: G 86 ASP cc_start: 0.5665 (OUTLIER) cc_final: 0.5240 (p0) REVERT: G 98 PHE cc_start: 0.9031 (m-10) cc_final: 0.8688 (m-80) REVERT: G 104 MET cc_start: 0.7139 (ttp) cc_final: 0.6707 (tmm) REVERT: G 118 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8834 (mm-30) REVERT: G 142 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7697 (mm-30) REVERT: G 164 MET cc_start: 0.8038 (mmm) cc_final: 0.7447 (mmt) REVERT: H 13 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8765 (mmmm) REVERT: H 118 TYR cc_start: 0.9075 (m-80) cc_final: 0.8828 (m-80) REVERT: H 143 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8727 (tm) REVERT: M 1347 MET cc_start: -0.3364 (ptt) cc_final: -0.4890 (mtt) REVERT: M 1350 MET cc_start: 0.3179 (OUTLIER) cc_final: 0.2930 (ppp) REVERT: Q 830 ARG cc_start: -0.0881 (ttt180) cc_final: -0.1189 (ptp-170) REVERT: Q 878 ARG cc_start: 0.7752 (tpt170) cc_final: 0.7316 (tpt-90) REVERT: W 11 GLN cc_start: 0.6936 (tp40) cc_final: 0.6431 (mp-120) REVERT: W 98 GLN cc_start: 0.2084 (tt0) cc_final: 0.1421 (tp40) REVERT: Y 63 MET cc_start: 0.6323 (tmm) cc_final: 0.6087 (tmm) REVERT: Y 64 MET cc_start: 0.7244 (mtp) cc_final: 0.6511 (mtm) REVERT: Z 197 MET cc_start: 0.8653 (ttt) cc_final: 0.7749 (tpt) REVERT: Z 254 MET cc_start: 0.8748 (ttt) cc_final: 0.8224 (mmm) REVERT: Z 474 MET cc_start: 0.6471 (mmm) cc_final: 0.6214 (mmp) REVERT: Z 486 GLU cc_start: 0.8726 (pt0) cc_final: 0.8421 (pm20) REVERT: Z 508 MET cc_start: 0.6745 (ttt) cc_final: 0.5965 (tpp) outliers start: 77 outliers final: 60 residues processed: 496 average time/residue: 0.5919 time to fit residues: 496.7364 Evaluate side-chains 475 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 407 time to evaluate : 5.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain M residue 1519 VAL Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 356 optimal weight: 0.0000 chunk 573 optimal weight: 30.0000 chunk 350 optimal weight: 0.3980 chunk 272 optimal weight: 6.9990 chunk 398 optimal weight: 9.9990 chunk 601 optimal weight: 1.9990 chunk 553 optimal weight: 10.0000 chunk 479 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 370 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN B 683 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS G 14 HIS ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1365 ASN ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 51256 Z= 0.166 Angle : 0.563 14.404 68951 Z= 0.284 Chirality : 0.043 0.211 6723 Planarity : 0.003 0.054 9154 Dihedral : 12.981 175.438 8568 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 1.71 % Allowed : 14.04 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 6303 helix: 1.73 (0.11), residues: 2293 sheet: -0.52 (0.17), residues: 890 loop : -0.91 (0.11), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1210 HIS 0.004 0.001 HIS B 98 PHE 0.032 0.001 PHE D 26 TYR 0.020 0.001 TYR G 3 ARG 0.007 0.000 ARG L 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12606 Ramachandran restraints generated. 6303 Oldfield, 0 Emsley, 6303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 414 time to evaluate : 5.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7638 (mmm-85) REVERT: A 301 HIS cc_start: 0.8039 (t70) cc_final: 0.7562 (t-170) REVERT: A 655 ILE cc_start: 0.9739 (OUTLIER) cc_final: 0.9429 (mp) REVERT: A 1221 MET cc_start: 0.8300 (mmm) cc_final: 0.7997 (mmm) REVERT: B 124 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9046 (pt) REVERT: B 240 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8957 (mm) REVERT: B 1081 ASP cc_start: 0.8713 (t70) cc_final: 0.8370 (t0) REVERT: D 38 HIS cc_start: 0.9382 (t70) cc_final: 0.9076 (t70) REVERT: D 62 MET cc_start: 0.8861 (mmp) cc_final: 0.8428 (mmm) REVERT: D 74 PHE cc_start: 0.5454 (OUTLIER) cc_final: 0.4760 (p90) REVERT: D 128 GLN cc_start: 0.9007 (mm110) cc_final: 0.8749 (mm110) REVERT: E 18 MET cc_start: 0.9000 (mmm) cc_final: 0.8739 (mmm) REVERT: G 2 PHE cc_start: 0.7807 (m-80) cc_final: 0.7520 (m-80) REVERT: G 44 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8813 (t80) REVERT: G 63 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7839 (mtp180) REVERT: G 80 PHE cc_start: 0.3802 (OUTLIER) cc_final: 0.3261 (m-80) REVERT: G 98 PHE cc_start: 0.9008 (m-10) cc_final: 0.8663 (m-80) REVERT: G 118 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8824 (mm-30) REVERT: G 142 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7729 (mm-30) REVERT: H 13 LYS cc_start: 0.9118 (mmmt) cc_final: 0.8714 (mmmm) REVERT: H 107 GLU cc_start: 0.8861 (pm20) cc_final: 0.8596 (pm20) REVERT: H 118 TYR cc_start: 0.9118 (m-80) cc_final: 0.8872 (m-80) REVERT: H 143 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8739 (tm) REVERT: M 1347 MET cc_start: -0.3359 (ptt) cc_final: -0.4879 (mtt) REVERT: M 1350 MET cc_start: 0.2984 (OUTLIER) cc_final: 0.2721 (ppp) REVERT: Q 763 ARG cc_start: 0.4190 (mmm-85) cc_final: 0.3921 (mmm-85) REVERT: Q 830 ARG cc_start: -0.0885 (ttt180) cc_final: -0.1187 (ptp-170) REVERT: Q 878 ARG cc_start: 0.7681 (tpt170) cc_final: 0.7019 (tpt-90) REVERT: W 11 GLN cc_start: 0.6958 (tp40) cc_final: 0.6486 (mp-120) REVERT: W 98 GLN cc_start: 0.2094 (tt0) cc_final: 0.1439 (tp40) REVERT: Y 63 MET cc_start: 0.6351 (tmm) cc_final: 0.6115 (tmm) REVERT: Y 64 MET cc_start: 0.7244 (mtp) cc_final: 0.6517 (mtm) REVERT: Z 197 MET cc_start: 0.8701 (ttt) cc_final: 0.7811 (tpt) REVERT: Z 254 MET cc_start: 0.8701 (ttt) cc_final: 0.8205 (mmm) REVERT: Z 474 MET cc_start: 0.6420 (mmm) cc_final: 0.6206 (mmp) REVERT: Z 486 GLU cc_start: 0.8723 (pt0) cc_final: 0.8422 (pm20) REVERT: Z 508 MET cc_start: 0.6719 (ttt) cc_final: 0.5961 (tpp) outliers start: 77 outliers final: 56 residues processed: 475 average time/residue: 0.6056 time to fit residues: 485.8029 Evaluate side-chains 460 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 396 time to evaluate : 5.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain M residue 1350 MET Chi-restraints excluded: chain M residue 1373 VAL Chi-restraints excluded: chain M residue 1515 TYR Chi-restraints excluded: chain M residue 1519 VAL Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Z residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 380 optimal weight: 2.9990 chunk 510 optimal weight: 50.0000 chunk 146 optimal weight: 4.9990 chunk 441 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 479 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 492 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.140102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.081098 restraints weight = 130645.331| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.33 r_work: 0.2787 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 465 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 467 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 51256 Z= 0.373 Angle : 0.622 14.668 68951 Z= 0.316 Chirality : 0.045 0.210 6723 Planarity : 0.003 0.054 9154 Dihedral : 13.020 174.734 8568 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 1.69 % Allowed : 14.22 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 6303 helix: 1.73 (0.11), residues: 2283 sheet: -0.65 (0.17), residues: 919 loop : -0.87 (0.11), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1210 HIS 0.005 0.001 HIS B 98 PHE 0.033 0.002 PHE A1388 TYR 0.033 0.001 TYR G 3 ARG 0.007 0.000 ARG Q 866 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12934.57 seconds wall clock time: 231 minutes 22.19 seconds (13882.19 seconds total)