Starting phenix.real_space_refine on Fri Sep 19 03:54:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9c_39859/09_2025/8z9c_39859_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9c_39859/09_2025/8z9c_39859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9c_39859/09_2025/8z9c_39859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9c_39859/09_2025/8z9c_39859.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9c_39859/09_2025/8z9c_39859_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9c_39859/09_2025/8z9c_39859_neut.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.049 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: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 89 5.49 5 S 95 5.16 5 C 14301 2.51 5 N 3995 2.21 5 O 4693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23182 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1154 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 153} Chain breaks: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1535 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1547 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "D" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1541 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1465 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 188} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1658 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4486 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 18, 'TRANS': 546} Chain breaks: 5 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 63 Chain: "I" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1330 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1532 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2182 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain breaks: 8 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 6, 'HIS:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 67 Chain: "L" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1320 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1003 Classifications: {'RNA': 48} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 24, 'rna3p': 23} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {' G%rna2p_pur:plan': 1, ' G%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 877 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna2p': 8, 'rna3p': 32} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 375 SG CYS A 71 33.614 55.852 184.378 1.00125.23 S ATOM 444 SG CYS A 81 30.838 55.036 181.981 1.00122.46 S ATOM 465 SG CYS A 84 30.069 57.529 184.598 1.00119.18 S ATOM 485 SG CYS A 87 32.391 58.529 181.904 1.00113.92 S ATOM 1704 SG CYS B 71 24.938 78.749 160.321 1.00 76.24 S ATOM 1778 SG CYS B 81 22.333 80.254 157.702 1.00 64.00 S ATOM 1819 SG CYS B 87 26.042 80.981 158.998 1.00 60.98 S ATOM 3241 SG CYS C 71 38.215 97.557 135.445 1.00 67.44 S ATOM 3315 SG CYS C 81 38.198 100.653 132.790 1.00 64.87 S ATOM 3336 SG CYS C 84 39.666 100.838 135.363 1.00 65.58 S ATOM 3356 SG CYS C 87 41.310 98.088 133.210 1.00 51.36 S ATOM 4788 SG CYS D 71 75.833 76.073 87.589 1.00 66.71 S ATOM 4862 SG CYS D 81 78.364 75.235 84.999 1.00 69.68 S ATOM 4883 SG CYS D 84 77.834 72.788 87.737 1.00 64.63 S ATOM 4903 SG CYS D 87 75.110 73.073 85.318 1.00 53.51 S ATOM 6331 SG CYS E 71 66.447 51.959 65.256 1.00 80.64 S ATOM 6405 SG CYS E 81 67.038 49.101 62.882 1.00 98.21 S ATOM 6426 SG CYS E 84 67.562 48.223 64.882 1.00 96.79 S ATOM 6446 SG CYS E 87 64.528 50.672 63.062 1.00 64.49 S ATOM 7861 SG CYS F 71 42.366 43.340 42.195 1.00108.96 S ATOM 7934 SG CYS F 84 39.271 43.962 44.503 1.00104.95 S ATOM 7954 SG CYS F 87 40.612 45.934 41.547 1.00 97.31 S ATOM 9309 SG CYS G 70 37.798 92.104 32.715 1.00124.51 S ATOM 9421 SG CYS G 85 40.802 92.369 31.454 1.00 30.00 S ATOM 9440 SG CYS G 88 40.679 95.321 34.203 1.00121.90 S ATOM 16800 SG CYS J 71 62.418 96.536 110.973 1.00 51.29 S ATOM 16874 SG CYS J 81 64.881 97.976 108.436 1.00 63.36 S ATOM 16895 SG CYS J 84 66.212 95.782 111.269 1.00 69.14 S ATOM 16915 SG CYS J 87 64.111 94.213 108.655 1.00 59.64 S Time building chain proxies: 4.51, per 1000 atoms: 0.19 Number of scatterers: 23182 At special positions: 0 Unit cell: (93.1, 122.55, 217.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 95 16.00 P 89 15.00 O 4693 8.00 N 3995 7.00 C 14301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 722.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 84 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 81 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 87 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 71 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 84 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 71 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 87 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 81 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 71 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 87 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 81 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 84 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 71 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 85 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 70 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 88 " pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 64 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 148 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 62 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " Number of angles added : 30 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 33 sheets defined 34.2% alpha, 18.9% beta 23 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 155 through 171 removed outlier: 4.743A pdb=" N SER A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.790A pdb=" N GLU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.638A pdb=" N GLY B 180 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 31 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.700A pdb=" N SER C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 166 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 30 Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.580A pdb=" N GLY D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.580A pdb=" N PHE D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 30 Processing helix chain 'E' and resid 51 through 67 removed outlier: 3.522A pdb=" N GLY E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 156 through 172 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.544A pdb=" N ARG E 197 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE E 198 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 51 through 67 Processing helix chain 'F' and resid 84 through 90 removed outlier: 3.656A pdb=" N LEU F 89 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 171 removed outlier: 4.574A pdb=" N SER F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 47 through 53 removed outlier: 4.084A pdb=" N ASP G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 127 through 142 Processing helix chain 'H' and resid 42 through 53 removed outlier: 3.959A pdb=" N GLY H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 86 through 107 removed outlier: 3.752A pdb=" N LEU H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASN H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 124 Processing helix chain 'H' and resid 207 through 221 removed outlier: 3.972A pdb=" N LEU H 211 " --> pdb=" O ASP H 207 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU H 220 " --> pdb=" O LYS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 245 removed outlier: 3.633A pdb=" N TYR H 240 " --> pdb=" O GLN H 236 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR H 245 " --> pdb=" O THR H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 268 Processing helix chain 'H' and resid 295 through 304 Processing helix chain 'H' and resid 322 through 333 removed outlier: 4.181A pdb=" N HIS H 326 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN H 329 " --> pdb=" O ASN H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 355 removed outlier: 3.566A pdb=" N LYS H 352 " --> pdb=" O THR H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 385 Processing helix chain 'H' and resid 399 through 413 Processing helix chain 'H' and resid 471 through 481 Processing helix chain 'H' and resid 509 through 523 Processing helix chain 'H' and resid 527 through 541 Processing helix chain 'H' and resid 541 through 554 Processing helix chain 'H' and resid 572 through 593 removed outlier: 3.860A pdb=" N LYS H 592 " --> pdb=" O LEU H 588 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR H 593 " --> pdb=" O SER H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 594 through 602 Processing helix chain 'I' and resid 470 through 488 removed outlier: 3.893A pdb=" N PHE I 474 " --> pdb=" O ASP I 470 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET I 476 " --> pdb=" O ASN I 472 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN I 488 " --> pdb=" O LYS I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 523 Processing helix chain 'I' and resid 527 through 541 Processing helix chain 'I' and resid 541 through 554 Processing helix chain 'I' and resid 572 through 592 removed outlier: 3.714A pdb=" N LYS I 592 " --> pdb=" O LEU I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 594 through 603 Processing helix chain 'J' and resid 24 through 32 Processing helix chain 'J' and resid 51 through 66 removed outlier: 3.551A pdb=" N ALA J 65 " --> pdb=" O ILE J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 90 Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 155 through 171 removed outlier: 4.662A pdb=" N SER J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 180 Processing helix chain 'J' and resid 196 through 199 Processing helix chain 'K' and resid 377 through 384 Processing helix chain 'K' and resid 401 through 413 Processing helix chain 'K' and resid 446 through 450 removed outlier: 4.104A pdb=" N SER K 449 " --> pdb=" O ASN K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 486 removed outlier: 3.770A pdb=" N PHE K 474 " --> pdb=" O ASP K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 523 Processing helix chain 'K' and resid 527 through 540 removed outlier: 3.614A pdb=" N LYS K 540 " --> pdb=" O GLU K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 553 removed outlier: 3.589A pdb=" N ALA K 545 " --> pdb=" O GLY K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 593 removed outlier: 3.788A pdb=" N LYS K 592 " --> pdb=" O LEU K 588 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR K 593 " --> pdb=" O SER K 589 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 603 Processing helix chain 'L' and resid 471 through 487 Processing helix chain 'L' and resid 511 through 523 Processing helix chain 'L' and resid 527 through 540 Processing helix chain 'L' and resid 542 through 554 Processing helix chain 'L' and resid 572 through 591 Processing helix chain 'L' and resid 594 through 603 Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 42 removed outlier: 5.150A pdb=" N LYS B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 47 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 42 removed outlier: 5.150A pdb=" N LYS B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 47 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 122 removed outlier: 4.039A pdb=" N ASP B 131 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 122 Processing sheet with id=AB1, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AB2, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.645A pdb=" N TYR D 9 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 122 removed outlier: 6.612A pdb=" N ARG D 115 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU D 136 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER D 117 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS D 134 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS D 119 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR D 132 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG D 121 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 122 removed outlier: 6.419A pdb=" N ARG E 115 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU E 136 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER E 117 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS E 134 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS E 119 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR E 132 " --> pdb=" O HIS E 119 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG E 121 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'F' and resid 143 through 145 removed outlier: 3.771A pdb=" N TYR F 9 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 189 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 122 removed outlier: 6.415A pdb=" N ARG F 115 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU F 136 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER F 117 " --> pdb=" O LYS F 134 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS F 134 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS F 119 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR F 132 " --> pdb=" O HIS F 119 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG F 121 " --> pdb=" O SER F 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 59 through 61 removed outlier: 4.204A pdb=" N VAL G 122 " --> pdb=" O LYS G 2 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 59 through 61 removed outlier: 4.204A pdb=" N VAL G 122 " --> pdb=" O LYS G 2 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 97 through 102 Processing sheet with id=AC3, first strand: chain 'H' and resid 2 through 4 removed outlier: 6.583A pdb=" N SER H 14 " --> pdb=" O CYS H 29 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS H 29 " --> pdb=" O SER H 14 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 57 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS H 58 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 139 through 142 Processing sheet with id=AC5, first strand: chain 'H' and resid 251 through 254 removed outlier: 6.731A pdb=" N VAL H 225 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER H 313 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 434 through 436 removed outlier: 6.477A pdb=" N LYS H 434 " --> pdb=" O ILE H 466 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE H 468 " --> pdb=" O LYS H 434 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL H 436 " --> pdb=" O ILE H 468 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ASP H 470 " --> pdb=" O VAL H 436 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG H 465 " --> pdb=" O LYS H 462 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 445 through 446 Processing sheet with id=AC8, first strand: chain 'I' and resid 436 through 437 removed outlier: 6.970A pdb=" N VAL I 436 " --> pdb=" O ILE I 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.781A pdb=" N ARG I 451 " --> pdb=" O GLU L 461 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL L 436 " --> pdb=" O ILE L 468 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ASP L 470 " --> pdb=" O VAL L 436 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 457 through 458 Processing sheet with id=AD2, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AD3, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AD4, first strand: chain 'J' and resid 114 through 122 removed outlier: 6.480A pdb=" N ARG J 115 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU J 136 " --> pdb=" O ARG J 115 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER J 117 " --> pdb=" O LYS J 134 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS J 134 " --> pdb=" O SER J 117 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS J 119 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR J 132 " --> pdb=" O HIS J 119 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG J 121 " --> pdb=" O SER J 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 141 through 143 removed outlier: 3.683A pdb=" N TYR K 191 " --> pdb=" O ASN K 163 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU K 195 " --> pdb=" O SER K 167 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU K 418 " --> pdb=" O VAL K 393 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 445 through 447 877 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 4.21 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4314 1.33 - 1.45: 6444 1.45 - 1.58: 12638 1.58 - 1.71: 176 1.71 - 1.83: 148 Bond restraints: 23720 Sorted by residual: bond pdb=" C THR J 109 " pdb=" N LYS J 110 " ideal model delta sigma weight residual 1.335 1.491 -0.156 1.31e-02 5.83e+03 1.42e+02 bond pdb=" C LEU J 177 " pdb=" N ASN J 178 " ideal model delta sigma weight residual 1.335 1.475 -0.140 1.38e-02 5.25e+03 1.03e+02 bond pdb=" C ASN H 522 " pdb=" N ILE H 523 " ideal model delta sigma weight residual 1.332 1.229 0.104 1.15e-02 7.56e+03 8.10e+01 bond pdb=" C ASN H 246 " pdb=" N PHE H 247 " ideal model delta sigma weight residual 1.330 1.208 0.122 1.37e-02 5.33e+03 7.96e+01 bond pdb=" C PHE G 51 " pdb=" N LEU G 52 " ideal model delta sigma weight residual 1.334 1.438 -0.103 1.27e-02 6.20e+03 6.64e+01 ... (remaining 23715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 30067 2.13 - 4.26: 1910 4.26 - 6.39: 297 6.39 - 8.53: 85 8.53 - 10.66: 20 Bond angle restraints: 32379 Sorted by residual: angle pdb=" N ILE H 523 " pdb=" CA ILE H 523 " pdb=" C ILE H 523 " ideal model delta sigma weight residual 112.90 104.98 7.92 9.60e-01 1.09e+00 6.81e+01 angle pdb=" O THR J 109 " pdb=" C THR J 109 " pdb=" N LYS J 110 " ideal model delta sigma weight residual 122.68 130.49 -7.81 1.17e+00 7.31e-01 4.46e+01 angle pdb=" CA MET K 508 " pdb=" C MET K 508 " pdb=" N SER K 509 " ideal model delta sigma weight residual 116.01 125.08 -9.07 1.41e+00 5.03e-01 4.13e+01 angle pdb=" C MET K 508 " pdb=" N SER K 509 " pdb=" CA SER K 509 " ideal model delta sigma weight residual 120.87 131.46 -10.59 1.69e+00 3.50e-01 3.92e+01 angle pdb=" CA ASN H 246 " pdb=" C ASN H 246 " pdb=" N PHE H 247 " ideal model delta sigma weight residual 114.76 121.73 -6.97 1.14e+00 7.69e-01 3.74e+01 ... (remaining 32374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 13936 35.57 - 71.14: 551 71.14 - 106.71: 54 106.71 - 142.28: 0 142.28 - 177.86: 3 Dihedral angle restraints: 14544 sinusoidal: 6643 harmonic: 7901 Sorted by residual: dihedral pdb=" O4' C N 2 " pdb=" C1' C N 2 " pdb=" N1 C N 2 " pdb=" C2 C N 2 " ideal model delta sinusoidal sigma weight residual 232.00 54.14 177.86 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C N -16 " pdb=" C1' C N -16 " pdb=" N1 C N -16 " pdb=" C2 C N -16 " ideal model delta sinusoidal sigma weight residual -128.00 48.47 -176.47 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 5 " pdb=" C1' U M 5 " pdb=" N1 U M 5 " pdb=" C2 U M 5 " ideal model delta sinusoidal sigma weight residual -128.00 44.43 -172.43 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 14541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3234 0.098 - 0.195: 444 0.195 - 0.293: 40 0.293 - 0.391: 11 0.391 - 0.488: 2 Chirality restraints: 3731 Sorted by residual: chirality pdb=" CB VAL H 460 " pdb=" CA VAL H 460 " pdb=" CG1 VAL H 460 " pdb=" CG2 VAL H 460 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CB ILE G 100 " pdb=" CA ILE G 100 " pdb=" CG1 ILE G 100 " pdb=" CG2 ILE G 100 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CB ILE G 163 " pdb=" CA ILE G 163 " pdb=" CG1 ILE G 163 " pdb=" CG2 ILE G 163 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 3728 not shown) Planarity restraints: 3835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP H 475 " -0.026 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" CG ASP H 475 " 0.096 2.00e-02 2.50e+03 pdb=" OD1 ASP H 475 " -0.035 2.00e-02 2.50e+03 pdb=" OD2 ASP H 475 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 68 " -0.028 2.00e-02 2.50e+03 5.36e-02 2.87e+01 pdb=" CD GLU F 68 " 0.093 2.00e-02 2.50e+03 pdb=" OE1 GLU F 68 " -0.033 2.00e-02 2.50e+03 pdb=" OE2 GLU F 68 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 158 " -0.024 2.00e-02 2.50e+03 5.09e-02 2.60e+01 pdb=" CD GLU K 158 " 0.088 2.00e-02 2.50e+03 pdb=" OE1 GLU K 158 " -0.031 2.00e-02 2.50e+03 pdb=" OE2 GLU K 158 " -0.033 2.00e-02 2.50e+03 ... (remaining 3832 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 776 2.68 - 3.24: 21201 3.24 - 3.79: 38775 3.79 - 4.35: 53359 4.35 - 4.90: 85299 Nonbonded interactions: 199410 Sorted by model distance: nonbonded pdb=" OD2 ASP H 169 " pdb="ZN ZN H 701 " model vdw 2.128 2.230 nonbonded pdb=" OG SER G 68 " pdb=" OE1 GLU G 90 " model vdw 2.182 3.040 nonbonded pdb=" OG1 THR B 42 " pdb=" O ASN B 45 " model vdw 2.215 3.040 nonbonded pdb=" OG SER C 16 " pdb=" O GLY C 180 " model vdw 2.226 3.040 nonbonded pdb=" NH2 ARG L 530 " pdb=" OP1 C N 28 " model vdw 2.254 3.120 ... (remaining 199405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 33 or (resid 34 through 35 and (name N or name CA \ or name C or name O or name CB )) or resid 36 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB )) or resid 76 or (resid 77 through \ 79 and (name N or name CA or name C or name O or name CB )) or resid 80 through \ 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 94 or (resid 95 through 96 and (name N or name CA or name C or nam \ e O or name CB )) or resid 97 through 154 or (resid 155 and (name N or name CA o \ r name C or name O or name CB )) or resid 156 through 192 or (resid 193 through \ 194 and (name N or name CA or name C or name O or name CB )) or resid 195 throug \ h 196 or resid 301)) selection = (chain 'C' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 33 or (resid 34 through 35 and (name N or name CA \ or name C or name O or name CB )) or resid 36 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB )) or resid 76 or (resid 77 through \ 79 and (name N or name CA or name C or name O or name CB )) or resid 80 through \ 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 94 or (resid 95 through 96 and (name N or name CA or name C or nam \ e O or name CB )) or resid 97 through 109 or (resid 110 and (name N or name CA o \ r name C or name O or name CB )) or resid 111 through 123 or (resid 124 and (nam \ e N or name CA or name C or name O or name CB )) or resid 125 through 154 or (re \ sid 155 and (name N or name CA or name C or name O or name CB )) or resid 156 th \ rough 192 or (resid 193 through 194 and (name N or name CA or name C or name O o \ r name CB )) or resid 195 through 196 or resid 301)) selection = (chain 'D' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 33 or (resid 34 through 35 and (name N or name CA \ or name C or name O or name CB )) or resid 36 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB )) or resid 76 or (resid 77 through \ 79 and (name N or name CA or name C or name O or name CB )) or resid 80 through \ 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 94 or (resid 95 through 96 and (name N or name CA or name C or nam \ e O or name CB )) or resid 97 through 109 or (resid 110 and (name N or name CA o \ r name C or name O or name CB )) or resid 111 through 123 or (resid 124 and (nam \ e N or name CA or name C or name O or name CB )) or resid 125 through 154 or (re \ sid 155 and (name N or name CA or name C or name O or name CB )) or resid 156 th \ rough 192 or (resid 193 through 194 and (name N or name CA or name C or name O o \ r name CB )) or resid 195 through 196 or resid 301)) selection = (chain 'E' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 33 or (resid 34 through 35 and (name N or name CA \ or name C or name O or name CB )) or resid 36 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB )) or resid 76 or (resid 77 through \ 79 and (name N or name CA or name C or name O or name CB )) or resid 80 through \ 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 94 or (resid 95 through 96 and (name N or name CA or name C or nam \ e O or name CB )) or resid 97 through 109 or (resid 110 and (name N or name CA o \ r name C or name O or name CB )) or resid 111 through 123 or (resid 124 and (nam \ e N or name CA or name C or name O or name CB )) or resid 125 through 154 or (re \ sid 155 and (name N or name CA or name C or name O or name CB )) or resid 156 th \ rough 196 or resid 301)) selection = (chain 'F' and (resid 3 through 33 or (resid 34 through 35 and (name N or name C \ A or name C or name O or name CB )) or resid 36 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 123 or ( \ resid 124 and (name N or name CA or name C or name O or name CB )) or resid 125 \ through 192 or (resid 193 through 194 and (name N or name CA or name C or name O \ or name CB )) or resid 195 through 301)) selection = (chain 'J' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 or (resid 77 through 79 and (na \ me N or name CA or name C or name O or name CB )) or resid 80 through 82 or (res \ id 83 and (name N or name CA or name C or name O or name CB )) or resid 84 throu \ gh 94 or (resid 95 through 96 and (name N or name CA or name C or name O or name \ CB )) or resid 97 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 123 or (resid 124 and (name N or name \ CA or name C or name O or name CB )) or resid 125 through 154 or (resid 155 and \ (name N or name CA or name C or name O or name CB )) or resid 156 through 192 o \ r (resid 193 through 194 and (name N or name CA or name C or name O or name CB ) \ ) or resid 195 through 196 or resid 301)) } ncs_group { reference = (chain 'I' and (resid 435 through 488 or resid 506 through 539 or (resid 540 and \ (name N or name CA or name C or name O or name CB )) or resid 541 through 546 o \ r (resid 547 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 48 through 577 or (resid 578 and (name N or name CA or name C or name O or name \ CB )) or resid 579 through 596 or (resid 597 and (name N or name CA or name C or \ name O or name CB )) or resid 598 through 607)) selection = (chain 'L' and (resid 435 through 461 or (resid 462 and (name N or name CA or na \ me C or name O or name CB )) or resid 463 through 607)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.880 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 23.550 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.009 0.322 23752 Z= 0.479 Angle : 1.265 51.582 32409 Z= 0.725 Chirality : 0.070 0.488 3731 Planarity : 0.009 0.111 3835 Dihedral : 18.283 177.856 9424 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.37 % Favored : 94.25 % Rotamer: Outliers : 0.70 % Allowed : 18.07 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.14), residues: 2661 helix: -1.40 (0.15), residues: 875 sheet: -2.19 (0.21), residues: 496 loop : -2.64 (0.14), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 34 TYR 0.048 0.003 TYR G 141 PHE 0.056 0.004 PHE I 458 TRP 0.025 0.003 TRP K 478 HIS 0.023 0.004 HIS H 373 Details of bonding type rmsd covalent geometry : bond 0.00902 (23720) covalent geometry : angle 1.18704 (32379) hydrogen bonds : bond 0.16481 ( 899) hydrogen bonds : angle 8.40037 ( 2636) metal coordination : bond 0.08124 ( 32) metal coordination : angle 14.44454 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 386 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7770 (tp30) REVERT: C 189 LYS cc_start: 0.8432 (mtpp) cc_final: 0.7828 (mttp) REVERT: F 156 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7618 (tptp) REVERT: G 141 TYR cc_start: 0.7985 (m-10) cc_final: 0.7722 (m-80) REVERT: G 195 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: I 568 GLU cc_start: 0.8183 (tt0) cc_final: 0.7608 (tt0) REVERT: J 5 MET cc_start: 0.8478 (mtm) cc_final: 0.8271 (mtp) REVERT: K 140 LYS cc_start: 0.7041 (mtpt) cc_final: 0.6050 (tptt) REVERT: L 462 LYS cc_start: 0.7088 (mttt) cc_final: 0.6541 (mttp) outliers start: 16 outliers final: 7 residues processed: 394 average time/residue: 0.1733 time to fit residues: 101.5054 Evaluate side-chains 358 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 350 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 453 MET Chi-restraints excluded: chain K residue 463 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0170 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 119 HIS F 36 ASN G 99 ASN H 107 ASN H 325 ASN I 443 ASN J 162 GLN J 171 ASN ** K 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 563 ASN L 479 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.168446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126514 restraints weight = 26281.831| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.46 r_work: 0.3180 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23752 Z= 0.135 Angle : 0.680 42.843 32409 Z= 0.314 Chirality : 0.042 0.294 3731 Planarity : 0.004 0.056 3835 Dihedral : 15.911 176.461 4289 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.80 % Favored : 96.02 % Rotamer: Outliers : 1.80 % Allowed : 17.15 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.15), residues: 2661 helix: 0.20 (0.17), residues: 892 sheet: -1.80 (0.21), residues: 503 loop : -2.29 (0.14), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 34 TYR 0.018 0.001 TYR G 137 PHE 0.021 0.002 PHE G 74 TRP 0.012 0.001 TRP L 535 HIS 0.006 0.001 HIS H 373 Details of bonding type rmsd covalent geometry : bond 0.00295 (23720) covalent geometry : angle 0.57374 (32379) hydrogen bonds : bond 0.03707 ( 899) hydrogen bonds : angle 5.27798 ( 2636) metal coordination : bond 0.00890 ( 32) metal coordination : angle 12.01333 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 375 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7634 (mtp) cc_final: 0.7409 (mtp) REVERT: A 51 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6687 (t80) REVERT: A 111 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: C 34 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7885 (ttp80) REVERT: C 189 LYS cc_start: 0.8452 (mtpp) cc_final: 0.7672 (mttp) REVERT: D 196 ASP cc_start: 0.8370 (p0) cc_final: 0.8110 (p0) REVERT: E 79 ARG cc_start: 0.8349 (ptp-170) cc_final: 0.7651 (mmp-170) REVERT: E 122 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8633 (mt) REVERT: E 197 ARG cc_start: 0.8063 (ptp90) cc_final: 0.7598 (ptp90) REVERT: F 156 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7042 (tptp) REVERT: G 88 CYS cc_start: 0.5836 (t) cc_final: 0.5248 (t) REVERT: G 90 GLU cc_start: 0.6308 (pt0) cc_final: 0.5634 (pm20) REVERT: G 159 LYS cc_start: 0.7682 (mtpt) cc_final: 0.7198 (mtmt) REVERT: H 225 VAL cc_start: 0.5665 (OUTLIER) cc_final: 0.5437 (p) REVERT: H 453 MET cc_start: 0.8001 (ttp) cc_final: 0.7677 (ptm) REVERT: I 453 MET cc_start: 0.8670 (ttp) cc_final: 0.8437 (ttp) REVERT: I 568 GLU cc_start: 0.8288 (tt0) cc_final: 0.7842 (tt0) REVERT: I 592 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8070 (ttmt) REVERT: J 5 MET cc_start: 0.8390 (mtm) cc_final: 0.8126 (mtp) REVERT: K 140 LYS cc_start: 0.6688 (mtpt) cc_final: 0.5601 (tttp) REVERT: K 551 GLN cc_start: 0.7952 (tt0) cc_final: 0.7552 (tm-30) REVERT: L 532 LYS cc_start: 0.6697 (ttpp) cc_final: 0.6195 (ttpt) REVERT: L 551 GLN cc_start: 0.7885 (tt0) cc_final: 0.7336 (tp40) outliers start: 41 outliers final: 17 residues processed: 395 average time/residue: 0.1765 time to fit residues: 103.0120 Evaluate side-chains 355 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 334 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 467 GLU Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 508 MET Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain L residue 470 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 237 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 260 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS G 99 ASN H 98 ASN H 325 ASN H 440 ASN J 125 GLN ** K 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.161028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119002 restraints weight = 26022.850| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.38 r_work: 0.3077 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23752 Z= 0.179 Angle : 0.607 26.130 32409 Z= 0.299 Chirality : 0.042 0.246 3731 Planarity : 0.004 0.041 3835 Dihedral : 15.522 177.036 4276 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.72 % Favored : 96.13 % Rotamer: Outliers : 2.11 % Allowed : 17.99 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.15), residues: 2661 helix: 0.95 (0.17), residues: 889 sheet: -1.53 (0.22), residues: 506 loop : -1.96 (0.15), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 183 TYR 0.012 0.001 TYR G 107 PHE 0.018 0.002 PHE G 74 TRP 0.010 0.001 TRP L 564 HIS 0.003 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00406 (23720) covalent geometry : angle 0.55732 (32379) hydrogen bonds : bond 0.03525 ( 899) hydrogen bonds : angle 4.67661 ( 2636) metal coordination : bond 0.00921 ( 32) metal coordination : angle 7.91948 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 376 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7422 (mtp) cc_final: 0.7146 (mtp) REVERT: A 51 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6560 (t80) REVERT: A 62 MET cc_start: 0.5707 (ttm) cc_final: 0.5488 (ttm) REVERT: C 34 ARG cc_start: 0.8297 (ttp-110) cc_final: 0.7953 (ttp80) REVERT: C 189 LYS cc_start: 0.8497 (mtpp) cc_final: 0.7681 (mttp) REVERT: D 196 ASP cc_start: 0.8541 (p0) cc_final: 0.8285 (p0) REVERT: E 69 ASN cc_start: 0.8544 (t0) cc_final: 0.8293 (t0) REVERT: E 79 ARG cc_start: 0.8505 (ptp-170) cc_final: 0.8299 (ptp-170) REVERT: E 122 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8888 (mt) REVERT: F 93 MET cc_start: 0.6519 (tpt) cc_final: 0.5829 (ptp) REVERT: F 156 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7474 (ttmm) REVERT: H 91 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7505 (mm-30) REVERT: H 115 TYR cc_start: 0.7558 (m-80) cc_final: 0.7316 (m-10) REVERT: H 453 MET cc_start: 0.8325 (ttp) cc_final: 0.8058 (ptm) REVERT: H 518 GLU cc_start: 0.8081 (tt0) cc_final: 0.7698 (tm-30) REVERT: I 524 LYS cc_start: 0.8332 (mttp) cc_final: 0.7783 (mmtt) REVERT: I 592 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8192 (ttmt) REVERT: J 5 MET cc_start: 0.8649 (mtm) cc_final: 0.8380 (mtp) REVERT: K 140 LYS cc_start: 0.6901 (mtpt) cc_final: 0.5911 (tttp) REVERT: K 412 SER cc_start: 0.8742 (m) cc_final: 0.8475 (t) REVERT: K 551 GLN cc_start: 0.8432 (tt0) cc_final: 0.8061 (tm-30) REVERT: L 471 LYS cc_start: 0.8072 (tppp) cc_final: 0.7815 (tptp) REVERT: L 551 GLN cc_start: 0.8140 (tt0) cc_final: 0.7610 (tp40) outliers start: 48 outliers final: 28 residues processed: 406 average time/residue: 0.1770 time to fit residues: 105.3427 Evaluate side-chains 363 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 333 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 511 ASP Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 470 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 105 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 258 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS C 152 ASN F 107 ASN J 125 GLN ** K 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112292 restraints weight = 26280.714| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.82 r_work: 0.2945 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 23752 Z= 0.335 Angle : 0.720 26.296 32409 Z= 0.353 Chirality : 0.047 0.242 3731 Planarity : 0.004 0.043 3835 Dihedral : 15.433 176.063 4276 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.28 % Favored : 95.57 % Rotamer: Outliers : 2.51 % Allowed : 19.44 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.15), residues: 2661 helix: 0.87 (0.17), residues: 895 sheet: -1.51 (0.22), residues: 501 loop : -1.89 (0.15), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 34 TYR 0.018 0.002 TYR G 137 PHE 0.026 0.002 PHE G 41 TRP 0.013 0.002 TRP D 176 HIS 0.004 0.001 HIS I 553 Details of bonding type rmsd covalent geometry : bond 0.00779 (23720) covalent geometry : angle 0.66876 (32379) hydrogen bonds : bond 0.03995 ( 899) hydrogen bonds : angle 4.81832 ( 2636) metal coordination : bond 0.01285 ( 32) metal coordination : angle 8.82665 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 349 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7353 (mtp) cc_final: 0.7152 (mtp) REVERT: A 51 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6489 (t80) REVERT: C 34 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.8070 (ttp80) REVERT: C 189 LYS cc_start: 0.8456 (mtpp) cc_final: 0.7728 (mttp) REVERT: D 196 ASP cc_start: 0.8574 (p0) cc_final: 0.8367 (p0) REVERT: E 25 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8434 (ttp-110) REVERT: E 69 ASN cc_start: 0.8536 (t0) cc_final: 0.8235 (t0) REVERT: E 79 ARG cc_start: 0.8542 (ptp-170) cc_final: 0.8277 (ptp-170) REVERT: F 156 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7497 (ttmm) REVERT: H 54 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7559 (ttmm) REVERT: H 236 GLN cc_start: 0.8282 (mp10) cc_final: 0.7943 (mp10) REVERT: H 453 MET cc_start: 0.8307 (ttp) cc_final: 0.7966 (ptm) REVERT: H 518 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: H 568 GLU cc_start: 0.8216 (tt0) cc_final: 0.7481 (mm-30) REVERT: J 5 MET cc_start: 0.8618 (mtm) cc_final: 0.8401 (mtp) REVERT: J 9 TYR cc_start: 0.9101 (m-80) cc_final: 0.8888 (m-80) REVERT: J 83 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.7805 (ptt-90) REVERT: K 140 LYS cc_start: 0.7011 (mtpt) cc_final: 0.5995 (tttp) REVERT: K 412 SER cc_start: 0.8754 (m) cc_final: 0.8549 (t) REVERT: K 485 MET cc_start: 0.8009 (tpp) cc_final: 0.7159 (mtt) REVERT: K 533 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7344 (mm-30) REVERT: L 471 LYS cc_start: 0.8021 (tppp) cc_final: 0.7715 (tptm) REVERT: L 551 GLN cc_start: 0.8329 (tt0) cc_final: 0.7885 (tp40) outliers start: 57 outliers final: 36 residues processed: 388 average time/residue: 0.1816 time to fit residues: 103.7571 Evaluate side-chains 363 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 325 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain H residue 269 ASN Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 518 GLU Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain I residue 562 ARG Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 470 ASP Chi-restraints excluded: chain L residue 525 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 20 optimal weight: 0.0270 chunk 202 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 18 optimal weight: 0.0670 chunk 113 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS F 32 GLN H 326 HIS ** K 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.161756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119909 restraints weight = 25956.359| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.35 r_work: 0.3084 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23752 Z= 0.108 Angle : 0.542 18.402 32409 Z= 0.276 Chirality : 0.041 0.268 3731 Planarity : 0.003 0.040 3835 Dihedral : 15.393 177.299 4276 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.84 % Rotamer: Outliers : 1.93 % Allowed : 20.93 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.16), residues: 2661 helix: 1.47 (0.18), residues: 886 sheet: -1.34 (0.21), residues: 516 loop : -1.62 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 25 TYR 0.015 0.001 TYR H 180 PHE 0.017 0.001 PHE G 41 TRP 0.015 0.001 TRP L 535 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00231 (23720) covalent geometry : angle 0.51143 (32379) hydrogen bonds : bond 0.03230 ( 899) hydrogen bonds : angle 4.35527 ( 2636) metal coordination : bond 0.00524 ( 32) metal coordination : angle 5.95777 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 359 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7223 (mtp) cc_final: 0.6965 (mtp) REVERT: A 51 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6579 (t80) REVERT: B 72 ASP cc_start: 0.7855 (t70) cc_final: 0.7610 (t0) REVERT: C 34 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.7997 (ttp80) REVERT: C 189 LYS cc_start: 0.8452 (mtpp) cc_final: 0.7791 (mttp) REVERT: E 25 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.8328 (ttp-110) REVERT: E 69 ASN cc_start: 0.8494 (t0) cc_final: 0.8190 (t0) REVERT: F 156 LYS cc_start: 0.7662 (mtpp) cc_final: 0.7429 (ttmm) REVERT: G 90 GLU cc_start: 0.6806 (pt0) cc_final: 0.6031 (pm20) REVERT: H 115 TYR cc_start: 0.7482 (m-10) cc_final: 0.7271 (m-10) REVERT: H 236 GLN cc_start: 0.8238 (mp10) cc_final: 0.7925 (mp10) REVERT: H 295 THR cc_start: 0.7925 (m) cc_final: 0.7381 (p) REVERT: H 518 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: H 568 GLU cc_start: 0.8165 (tt0) cc_final: 0.7569 (mm-30) REVERT: I 578 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8408 (ttmm) REVERT: I 597 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8090 (mtmm) REVERT: J 5 MET cc_start: 0.8401 (mtm) cc_final: 0.8089 (mtp) REVERT: J 123 GLU cc_start: 0.8091 (tt0) cc_final: 0.7683 (tp30) REVERT: K 140 LYS cc_start: 0.6978 (mtpt) cc_final: 0.6054 (tttp) REVERT: K 485 MET cc_start: 0.7708 (tpp) cc_final: 0.7132 (mtt) REVERT: K 518 GLU cc_start: 0.7956 (tt0) cc_final: 0.7410 (tm-30) REVERT: L 462 LYS cc_start: 0.7319 (mttt) cc_final: 0.7045 (mttt) REVERT: L 471 LYS cc_start: 0.7921 (tppp) cc_final: 0.7658 (tptm) REVERT: L 551 GLN cc_start: 0.8296 (tt0) cc_final: 0.7864 (tp40) outliers start: 44 outliers final: 28 residues processed: 387 average time/residue: 0.1759 time to fit residues: 100.1520 Evaluate side-chains 352 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 321 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 269 ASN Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 518 GLU Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 467 GLU Chi-restraints excluded: chain I residue 597 LYS Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 470 ASP Chi-restraints excluded: chain L residue 525 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 203 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 194 optimal weight: 0.5980 chunk 139 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS F 107 ASN J 125 GLN ** K 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114916 restraints weight = 26328.598| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.84 r_work: 0.2987 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23752 Z= 0.206 Angle : 0.587 21.802 32409 Z= 0.291 Chirality : 0.042 0.233 3731 Planarity : 0.003 0.040 3835 Dihedral : 15.268 176.631 4273 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.61 % Favored : 96.32 % Rotamer: Outliers : 2.29 % Allowed : 21.06 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.16), residues: 2661 helix: 1.57 (0.18), residues: 885 sheet: -1.22 (0.22), residues: 514 loop : -1.56 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 34 TYR 0.015 0.001 TYR H 180 PHE 0.023 0.002 PHE G 41 TRP 0.016 0.001 TRP H 478 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00477 (23720) covalent geometry : angle 0.54805 (32379) hydrogen bonds : bond 0.03257 ( 899) hydrogen bonds : angle 4.39413 ( 2636) metal coordination : bond 0.00843 ( 32) metal coordination : angle 6.88786 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 334 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7173 (mtp) cc_final: 0.6950 (mtp) REVERT: A 51 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6552 (t80) REVERT: C 34 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.8078 (ttp80) REVERT: C 189 LYS cc_start: 0.8440 (mtpp) cc_final: 0.7736 (mttp) REVERT: D 111 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: E 25 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8345 (ttp-110) REVERT: E 69 ASN cc_start: 0.8497 (t0) cc_final: 0.8171 (t0) REVERT: E 189 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7666 (tttt) REVERT: F 156 LYS cc_start: 0.7696 (mtpp) cc_final: 0.7486 (ttmm) REVERT: G 90 GLU cc_start: 0.6803 (pt0) cc_final: 0.5977 (pm20) REVERT: H 129 ASP cc_start: 0.8247 (p0) cc_final: 0.8015 (p0) REVERT: H 236 GLN cc_start: 0.8343 (mp10) cc_final: 0.8003 (mp10) REVERT: H 295 THR cc_start: 0.8027 (m) cc_final: 0.7451 (p) REVERT: H 518 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: H 568 GLU cc_start: 0.8188 (tt0) cc_final: 0.7580 (mm-30) REVERT: I 578 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8456 (ttmm) REVERT: J 5 MET cc_start: 0.8560 (mtm) cc_final: 0.8283 (mtp) REVERT: J 123 GLU cc_start: 0.8153 (tt0) cc_final: 0.7736 (tp30) REVERT: K 485 MET cc_start: 0.7711 (tpp) cc_final: 0.7182 (mtt) REVERT: L 462 LYS cc_start: 0.7442 (mttt) cc_final: 0.7068 (mttt) REVERT: L 471 LYS cc_start: 0.8011 (tppp) cc_final: 0.7682 (tptm) REVERT: L 551 GLN cc_start: 0.8324 (tt0) cc_final: 0.7910 (tp40) outliers start: 52 outliers final: 40 residues processed: 369 average time/residue: 0.1839 time to fit residues: 100.0198 Evaluate side-chains 364 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 269 ASN Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 518 GLU Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 562 ARG Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 470 ASP Chi-restraints excluded: chain L residue 525 ILE Chi-restraints excluded: chain L residue 590 LEU Chi-restraints excluded: chain L residue 601 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 206 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 247 optimal weight: 0.2980 chunk 272 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS F 107 ASN ** K 488 GLN ** 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 = 0.3877 r_free = 0.3877 target = 0.159943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115966 restraints weight = 26117.106| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.71 r_work: 0.3011 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23752 Z= 0.168 Angle : 0.561 20.949 32409 Z= 0.281 Chirality : 0.041 0.239 3731 Planarity : 0.003 0.040 3835 Dihedral : 15.266 176.599 4273 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 2.55 % Allowed : 20.93 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.16), residues: 2661 helix: 1.71 (0.18), residues: 885 sheet: -1.12 (0.22), residues: 514 loop : -1.47 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 34 TYR 0.016 0.001 TYR H 180 PHE 0.025 0.001 PHE G 41 TRP 0.016 0.001 TRP L 535 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00387 (23720) covalent geometry : angle 0.52520 (32379) hydrogen bonds : bond 0.03142 ( 899) hydrogen bonds : angle 4.29249 ( 2636) metal coordination : bond 0.00716 ( 32) metal coordination : angle 6.51423 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 330 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7114 (mtp) cc_final: 0.6857 (mtp) REVERT: A 51 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6527 (t80) REVERT: C 34 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.8074 (ttp80) REVERT: C 189 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7778 (mttp) REVERT: D 111 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: D 196 ASP cc_start: 0.8693 (p0) cc_final: 0.8447 (p0) REVERT: E 69 ASN cc_start: 0.8491 (t0) cc_final: 0.8155 (t0) REVERT: E 79 ARG cc_start: 0.8502 (ptp-170) cc_final: 0.8288 (ptp-170) REVERT: E 189 LYS cc_start: 0.7842 (ttpt) cc_final: 0.7638 (tttt) REVERT: G 7 ILE cc_start: 0.7813 (mt) cc_final: 0.7457 (mt) REVERT: G 39 ILE cc_start: 0.8324 (mm) cc_final: 0.8092 (mm) REVERT: G 90 GLU cc_start: 0.6797 (pt0) cc_final: 0.5950 (pm20) REVERT: H 129 ASP cc_start: 0.8206 (p0) cc_final: 0.7977 (p0) REVERT: H 236 GLN cc_start: 0.8329 (mp10) cc_final: 0.7989 (mp10) REVERT: H 257 MET cc_start: 0.7796 (ttt) cc_final: 0.7520 (ttt) REVERT: H 295 THR cc_start: 0.8049 (m) cc_final: 0.7480 (p) REVERT: H 518 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: H 568 GLU cc_start: 0.8166 (tt0) cc_final: 0.7639 (mm-30) REVERT: I 578 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8497 (ttmm) REVERT: J 5 MET cc_start: 0.8535 (mtm) cc_final: 0.8267 (mtp) REVERT: J 123 GLU cc_start: 0.8140 (tt0) cc_final: 0.7702 (tp30) REVERT: K 140 LYS cc_start: 0.6925 (mtmt) cc_final: 0.5958 (tttp) REVERT: K 450 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.5828 (t80) REVERT: K 485 MET cc_start: 0.7568 (tpp) cc_final: 0.7114 (mtt) REVERT: L 462 LYS cc_start: 0.7505 (mttt) cc_final: 0.7140 (mttt) REVERT: L 471 LYS cc_start: 0.7995 (tppp) cc_final: 0.7667 (tptm) REVERT: L 510 HIS cc_start: 0.7109 (t70) cc_final: 0.6899 (t-90) REVERT: L 551 GLN cc_start: 0.8349 (tt0) cc_final: 0.7941 (tp40) outliers start: 58 outliers final: 43 residues processed: 373 average time/residue: 0.1728 time to fit residues: 95.7334 Evaluate side-chains 369 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 269 ASN Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 518 GLU Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 439 ILE Chi-restraints excluded: chain I residue 562 ARG Chi-restraints excluded: chain I residue 597 LYS Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 450 TYR Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 470 ASP Chi-restraints excluded: chain L residue 525 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 139 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 186 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 212 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS H 326 HIS ** K 488 GLN ** 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 = 0.3896 r_free = 0.3896 target = 0.161532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119673 restraints weight = 25900.494| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.42 r_work: 0.3077 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23752 Z= 0.115 Angle : 0.527 17.705 32409 Z= 0.268 Chirality : 0.040 0.257 3731 Planarity : 0.003 0.040 3835 Dihedral : 15.246 177.114 4273 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 2.07 % Allowed : 21.20 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.16), residues: 2661 helix: 1.92 (0.18), residues: 889 sheet: -1.09 (0.22), residues: 525 loop : -1.33 (0.16), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 25 TYR 0.013 0.001 TYR G 137 PHE 0.027 0.001 PHE G 41 TRP 0.021 0.001 TRP L 535 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00259 (23720) covalent geometry : angle 0.49911 (32379) hydrogen bonds : bond 0.02999 ( 899) hydrogen bonds : angle 4.12845 ( 2636) metal coordination : bond 0.00509 ( 32) metal coordination : angle 5.62352 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 339 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7103 (mtp) cc_final: 0.6860 (mtp) REVERT: A 51 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6519 (t80) REVERT: C 34 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.8056 (ttp80) REVERT: C 189 LYS cc_start: 0.8429 (mtpp) cc_final: 0.7783 (mttp) REVERT: D 111 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: E 25 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8364 (ttp-110) REVERT: E 69 ASN cc_start: 0.8530 (t0) cc_final: 0.8186 (t0) REVERT: E 79 ARG cc_start: 0.8461 (ptp-170) cc_final: 0.8240 (ptp-170) REVERT: E 155 GLU cc_start: 0.7954 (pm20) cc_final: 0.7749 (pm20) REVERT: E 189 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7707 (tttt) REVERT: G 7 ILE cc_start: 0.7908 (mt) cc_final: 0.7619 (mt) REVERT: G 39 ILE cc_start: 0.8323 (mm) cc_final: 0.8118 (mm) REVERT: H 129 ASP cc_start: 0.8105 (p0) cc_final: 0.7895 (p0) REVERT: H 236 GLN cc_start: 0.8307 (mp10) cc_final: 0.7992 (mp10) REVERT: H 257 MET cc_start: 0.7756 (ttt) cc_final: 0.7521 (ttt) REVERT: H 275 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7907 (ttpt) REVERT: H 295 THR cc_start: 0.7995 (m) cc_final: 0.7433 (p) REVERT: H 317 MET cc_start: 0.7340 (mpp) cc_final: 0.6772 (mpp) REVERT: H 518 GLU cc_start: 0.7948 (tt0) cc_final: 0.7682 (tm-30) REVERT: H 568 GLU cc_start: 0.8153 (tt0) cc_final: 0.7693 (mm-30) REVERT: J 5 MET cc_start: 0.8449 (mtm) cc_final: 0.8140 (mtp) REVERT: J 83 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.7977 (ptt-90) REVERT: J 123 GLU cc_start: 0.8092 (tt0) cc_final: 0.7682 (tp30) REVERT: K 140 LYS cc_start: 0.7013 (mtmt) cc_final: 0.6064 (tttp) REVERT: K 450 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.5908 (t80) REVERT: K 485 MET cc_start: 0.7377 (tpp) cc_final: 0.7136 (mtt) REVERT: K 518 GLU cc_start: 0.7997 (tt0) cc_final: 0.7475 (tm-30) REVERT: L 471 LYS cc_start: 0.7919 (tppp) cc_final: 0.7607 (tptm) REVERT: L 551 GLN cc_start: 0.8322 (tt0) cc_final: 0.7909 (tp40) outliers start: 47 outliers final: 35 residues processed: 373 average time/residue: 0.1779 time to fit residues: 97.8917 Evaluate side-chains 356 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 269 ASN Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain I residue 597 LYS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain K residue 450 TYR Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 470 ASP Chi-restraints excluded: chain L residue 525 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 193 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS F 107 ASN I 516 ASN ** K 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113488 restraints weight = 26230.285| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.10 r_work: 0.2949 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 23752 Z= 0.300 Angle : 0.668 24.360 32409 Z= 0.329 Chirality : 0.045 0.219 3731 Planarity : 0.004 0.053 3835 Dihedral : 15.162 176.662 4273 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 2.29 % Allowed : 21.02 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.16), residues: 2661 helix: 1.67 (0.17), residues: 881 sheet: -1.06 (0.22), residues: 513 loop : -1.43 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 121 TYR 0.017 0.002 TYR H 180 PHE 0.029 0.002 PHE G 41 TRP 0.016 0.002 TRP L 535 HIS 0.023 0.002 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00699 (23720) covalent geometry : angle 0.62680 (32379) hydrogen bonds : bond 0.03581 ( 899) hydrogen bonds : angle 4.44013 ( 2636) metal coordination : bond 0.01153 ( 32) metal coordination : angle 7.62575 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 322 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6609 (t80) REVERT: C 189 LYS cc_start: 0.8435 (mtpp) cc_final: 0.7712 (mttp) REVERT: D 111 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: E 25 ARG cc_start: 0.8621 (ttp80) cc_final: 0.8356 (ttp-110) REVERT: H 129 ASP cc_start: 0.8286 (p0) cc_final: 0.8042 (p0) REVERT: H 236 GLN cc_start: 0.8368 (mp10) cc_final: 0.8038 (mp10) REVERT: H 257 MET cc_start: 0.7750 (ttt) cc_final: 0.7497 (ttt) REVERT: H 518 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: H 568 GLU cc_start: 0.8234 (tt0) cc_final: 0.7673 (mm-30) REVERT: J 5 MET cc_start: 0.8590 (mtm) cc_final: 0.8377 (mtp) REVERT: K 450 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.5769 (t80) REVERT: K 485 MET cc_start: 0.7611 (tpp) cc_final: 0.7238 (mtt) REVERT: L 471 LYS cc_start: 0.8021 (tppp) cc_final: 0.7669 (tptm) REVERT: L 551 GLN cc_start: 0.8431 (tt0) cc_final: 0.8027 (tp40) outliers start: 52 outliers final: 42 residues processed: 355 average time/residue: 0.1736 time to fit residues: 91.2483 Evaluate side-chains 359 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain H residue 269 ASN Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 518 GLU Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 549 ILE Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 562 ARG Chi-restraints excluded: chain I residue 597 LYS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain K residue 450 TYR Chi-restraints excluded: chain K residue 551 GLN Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 470 ASP Chi-restraints excluded: chain L residue 525 ILE Chi-restraints excluded: chain L residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 196 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 187 optimal weight: 0.5980 chunk 233 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS D 171 ASN ** K 488 GLN ** 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 = 0.3856 r_free = 0.3856 target = 0.157991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115869 restraints weight = 26133.991| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.53 r_work: 0.3032 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 23752 Z= 0.155 Angle : 0.566 20.746 32409 Z= 0.285 Chirality : 0.042 0.235 3731 Planarity : 0.003 0.041 3835 Dihedral : 15.249 176.942 4273 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.84 % Rotamer: Outliers : 2.07 % Allowed : 21.42 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2661 helix: 1.80 (0.17), residues: 885 sheet: -1.06 (0.22), residues: 514 loop : -1.39 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 25 TYR 0.018 0.001 TYR G 137 PHE 0.029 0.001 PHE G 41 TRP 0.042 0.001 TRP L 535 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00360 (23720) covalent geometry : angle 0.53154 (32379) hydrogen bonds : bond 0.03151 ( 899) hydrogen bonds : angle 4.28280 ( 2636) metal coordination : bond 0.00716 ( 32) metal coordination : angle 6.45934 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6554 (t80) REVERT: C 189 LYS cc_start: 0.8413 (mtpp) cc_final: 0.7807 (mttp) REVERT: D 111 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: D 196 ASP cc_start: 0.8705 (p0) cc_final: 0.8503 (p0) REVERT: E 25 ARG cc_start: 0.8614 (ttp80) cc_final: 0.8361 (ttp-110) REVERT: E 79 ARG cc_start: 0.8456 (ptp-170) cc_final: 0.8245 (ptp-170) REVERT: G 7 ILE cc_start: 0.7926 (mt) cc_final: 0.7547 (mt) REVERT: H 129 ASP cc_start: 0.8227 (p0) cc_final: 0.7988 (p0) REVERT: H 236 GLN cc_start: 0.8303 (mp10) cc_final: 0.7995 (mp10) REVERT: H 257 MET cc_start: 0.7705 (ttt) cc_final: 0.7465 (ttt) REVERT: H 295 THR cc_start: 0.8091 (m) cc_final: 0.7527 (p) REVERT: H 518 GLU cc_start: 0.8016 (tt0) cc_final: 0.7738 (tm-30) REVERT: H 568 GLU cc_start: 0.8203 (tt0) cc_final: 0.7776 (mm-30) REVERT: J 5 MET cc_start: 0.8532 (mtm) cc_final: 0.8279 (mtp) REVERT: J 123 GLU cc_start: 0.8106 (tt0) cc_final: 0.7697 (tp30) REVERT: K 450 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.5797 (t80) REVERT: K 485 MET cc_start: 0.7352 (tpp) cc_final: 0.7145 (mtt) REVERT: K 518 GLU cc_start: 0.8025 (tt0) cc_final: 0.7502 (tm-30) REVERT: L 471 LYS cc_start: 0.7992 (tppp) cc_final: 0.7672 (tptm) REVERT: L 551 GLN cc_start: 0.8423 (tt0) cc_final: 0.8051 (tp40) outliers start: 47 outliers final: 35 residues processed: 348 average time/residue: 0.1787 time to fit residues: 92.3034 Evaluate side-chains 348 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 269 ASN Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 603 ILE Chi-restraints excluded: chain I residue 597 LYS Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain K residue 450 TYR Chi-restraints excluded: chain L residue 455 PHE Chi-restraints excluded: chain L residue 470 ASP Chi-restraints excluded: chain L residue 525 ILE Chi-restraints excluded: chain L residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 30 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 216 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 253 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS H 326 HIS ** K 488 GLN ** 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 = 0.3901 r_free = 0.3901 target = 0.161749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118115 restraints weight = 26096.169| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.44 r_work: 0.3071 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23752 Z= 0.125 Angle : 0.538 17.824 32409 Z= 0.274 Chirality : 0.041 0.251 3731 Planarity : 0.003 0.040 3835 Dihedral : 15.213 177.547 4272 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 1.85 % Allowed : 22.08 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 2661 helix: 2.01 (0.18), residues: 886 sheet: -1.01 (0.22), residues: 525 loop : -1.30 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 25 TYR 0.016 0.001 TYR H 180 PHE 0.028 0.001 PHE G 41 TRP 0.030 0.001 TRP L 535 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00284 (23720) covalent geometry : angle 0.51009 (32379) hydrogen bonds : bond 0.02983 ( 899) hydrogen bonds : angle 4.12031 ( 2636) metal coordination : bond 0.00515 ( 32) metal coordination : angle 5.61469 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5202.40 seconds wall clock time: 89 minutes 56.55 seconds (5396.55 seconds total)